JEOL Resources

1.8 Å resolution structure of β-galactosidase with a 200 kV CRYO ARM electron microscope

Thu, 10 Dec 2020 11:35:20 GMT

See IUCrJ Volume 7, July 2020, pages 639-643.

A New Take on the Phase Plate

Thu, 10 Dec 2020 11:40:13 GMT

TEM phase plate development was extensively pursued by Prof Nagayama’s lab in Japan for over ten years. Prof Chiu of Baylor College of Medicine has successfully applied the phase plate system on his Omega filtered TEM (JEM-2200FS) to the molecular structure characterization for proteins.

A reprint from Lab Product News.

Ad-hoc Auto Tuning

Thu, 10 Dec 2020 11:09:18 GMT

Auto Tuning for HR-STEM for crystalline sample.

Atomic resolution structure results from the JEOL 200 kV CRYO ARM™ TEM

Thu, 10 Dec 2020 11:12:35 GMT

High resolution structure determination by electron cryo-microscopy (cryoEM) and Single Particle Analysis (SPA) has progressed to the point where structures can be determined routinely to better than 3Å on a 300 kV microscope. Pioneering efforts have shown that similar results can also be achieved on 200 kV platforms. Similarly, efforts are underway to allow for a structure determination within a single day or even less. Here, we show results from Merk et al. at NIH from the JEOL CRYO ARM™ 200 obtained on beta-galactosidase at 1.8Å resolution1. The 3D map shows surprising details in the map reflecting the high resolution quality of the data.

Atomic resolution structures of biological macromolecules using microED on JEOL TEMs

Wed, 09 Dec 2020 13:23:39 GMT

Also see: JEOL CRYO ARM™ Achieves Top Resolution August 2023.

Micro electron diffraction, or microED, is a technique aimed at solving structures of biological macromolecules by electron diffraction. Barn-storming work by the group from Prof. Gonen showed the impressive impact and promise of this technique¹. The technique borrows from X-ray crystallography in that precession techniques are used for data collection and that much of the well-established software for solving structures by X-ray crystallography can be used for microED. However, it differs in a fundamental way in that electrons are used, which, owing to the substantially larger scattering cross-section of electrons with biological matter, means much smaller crystals can be used. Thus, crystals the size of a few microns are perfectly adequate for microED. The current crop of cameras and levels of microscope automation allow for the rapid collection of a full data set in a matter of minutes. By combining microED with the principle steps of SPA as employed in SerialEM², a single overnight run can yield hundreds of microED data sets³. Note that because diffraction data is collected, the acquisition process is immune to mechanical vibrations and drift; only a shift caused by poor eucentricity that would move the crystal out of the selected aperture field of view would impact the data collection.

MicroED can be applied on every new electron microscope in the JEOL TEM line-up. Precise control of the goniometer’s tilting speed compatible with microED is standard and can be set through either SerialEM or Recorder, the latter being part of JEOL’s TEMography package (SIF). SerialEM was first introduced on a JEOL JEM-2200FS in 2006 and is now fully compatible with all of JEOL’s electron microscopes. A record-breaking 1.34Å structure of apo-ferritin was recently obtained from JEOL’s latest generation of cryo-TEMs, the CRYO ARM™, a microscope available at 200 and 300 kV with a cold field emission gun and in-column energy filter⁴.

This application note reports on microED results obtained on a JEOL JEM-F200 outfitted with a cold FEG and a Gatan Elsa holder to keep the sample at -177ºC for the sake of reducing radiation damage⁵. Figure 1 shows a gallery of principle checks whether crystals of L-histidine will deliver high-resolution diffraction patterns for microED. The micro-crystals are deposited on ultrathin carbon films overlaid on lacey carbon.

Fig. 1: Diffraction images of L-histidine in defocused diffraction mode without (left) and with (middle) a selected area aperture inserted showing the L-histidine crystals. The focused diffraction pattern is shown on the right showing strong Bragg reflections.

Figure 2 shows several frames from one of the microED data sets acquired under continuous rotation at 0.25º/sec from -30º to +30º. The beam stopper is used to prevent the central, undiffracted beam from hitting the camera’s sensor.

Fig. 2: Selected focused diffraction patterns from -30º to +30º microED series acquired at 0.25º/sec. Total dose was 2.4 el/Å2.

After unpacking the movies, the individual frames are processed using standard X-ray crystallographic packages – SIR2019 and SHELXL. Table 1 shows the experimental results whereas Figure 3 shows the structures calculated from the data using direct methods. The refined map after running SHELXL shows clearly the expected atoms in the structure.

Table 1: experimental results
Molecular weight (Da)	155.16
Measurement temperature (K)	96
Space group	P212121
a, b, c (Å)	5.27, 7.44, 18.99
# of reflections	417
R factor (%)	19.81

Fig 3: Structure of L-histidine after initial direct method calculation using SIR2019 (left) and after refinement using SHELXL (middle) with the structure formula shown right.

Conclusion: Micro electron diffraction data can be readily acquired using a JEOL cryo-electron microscope using relatively shallow tilt series. The resulting data can immediately be processed using available pipe lines for X-ray diffraction data enabling rapid structure determination of small molecules by electron diffraction.

Contact your local JEOL representative to learn more about JEOL TEMs and microED using SIF Recorder or SerialEM.

References:

B.L. Nannenga et al., Nature Methods 11 (2014) 927.
D.N. Mastronarde, J. Struct. Biol. 152 (2005) 36.
M.J. de la Cruz et al., Ultramicroscopy 201 (2019) 77.
M. Tegunov et al. (2020) https://doi.org/10.1101/2020.06.05.136341.
Guzmán-Afonso et al., Nature Comm 10 (2019) 3537.

CRYO ARM Bibliography

Wed, 17 Sep 2025 11:56:00 GMT

JEOL CRYOARM - BIBLIOGRAPHY

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Kishikawa, J et al. “Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases.” Nature communications vol. 13,1 1213. 8 Mar. 2022, doi:10.1038/s41467-022-28832-5
Hogrel, Gaëlle et al. “Cyclic nucleotide-induced helical structure activates a TIR immune effector.” Nature vol. 608,7924 (2022): 808-812. doi:10.1038/s41586-022-05070-9
Kiss-Szemán, Anna J et al. “Cryo-EM structure of acylpeptide hydrolase reveals substrate selection by multimerization and a multi-state serine-protease triad.” Chemical science vol. 13,24 7132-7142. 18 May. 2022, doi:10.1039/d2sc02276a
Shi, Yun et al. “Structural basis of SARM1 activation, substrate recognition, and inhibition by small molecules.” Molecular cell vol. 82,9 (2022): 1643-1659.e10. doi:10.1016/j.molcel.2022.03.007
Tani, Kazutoshi et al. “A Ca2+-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes.” The Journal of biological chemistry vol. 298,6 (2022): 101967. doi:10.1016/j.jbc.2022.101967
Watanabe, Ryoto et al. “Particle Morphology of Medusavirus Inside and Outside the Cells Reveals a New Maturation Process of Giant Viruses.” Journal of virology vol. 96,7 (2022): e0185321. doi:10.1128/jvi.01853-21
Kato, Koji et al. “Structural basis for the absence of low-energy chlorophylls in a photosystem I trimer from Gloeobacter violaceus.” eLife vol. 11 e73990. 11 Apr. 2022, doi:10.7554/eLife.73990
Li, Na et al. “Cryo-EM structure of glycoprotein C from Crimean-Congo hemorrhagic fever virus.” Virologica Sinica vol. 37,1 (2022): 127-137. doi:10.1016/j.virs.2022.01.015
Tanaka, Saki et al. “Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump.” Journal of medicinal chemistry vol. 65,11 (2022): 7843-7853. doi:10.1021/acs.jmedchem.2c00338
Gfrerer, Sabrina et al. “A Micrarchaeon Isolate Is Covered by a Proteinaceous S-Layer.” Applied and environmental microbiology vol. 88,5 (2022): e0155321. doi:10.1128/AEM.01553-21
Kuzuya, Maki et al. “Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids.” Science signaling vol. 15,720 (2022): eabg6941. doi:10.1126/scisignal.abg6941
Kolata, Piotr, and Rouslan G Efremov. “Structure of Escherichia coli respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation.” eLife vol. 10 e68710. 26 Jul. 2021, doi:10.7554/eLife.68710
Yamaguchi, Tomoko et al. “Structure of the molecular bushing of the bacterial flagellar motor.” Nature communications vol. 12,1 4469. 22 Jul. 2021, doi:10.1038/s41467-021-24715-3
Yu, Huaxin et al. “Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer.” Biochimica et biophysica acta. Bioenergetics vol. 1862,10 (2021): 148471. doi:10.1016/j.bbabio.2021.148471
Hiragi, Keito et al. “Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.” Journal of structural biology vol. 213,3 (2021): 107748. doi:10.1016/j.jsb.2021.107748
Kawamoto, Akihiro et al. “Native flagellar MS ring is formed by 34 subunits with 23-fold and 11-fold subsymmetries.” Nature communications vol. 12,1 4223. 9 Jul. 2021, doi:10.1038/s41467-021-24507-9
Pradhan, Brajabandhu et al. “Endospore Appendages: a novel pilus superfamily from the endospores of pathogenic Bacilli.” The EMBO journal vol. 40,17 (2021): e106887. doi:10.15252/embj.2020106887
Efremov, Rouslan G, and Annelore Stroobants. “Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300.” Acta crystallographica. Section D, Structural biology vol. 77,Pt 5 (2021): 555-564. doi:10.1107/S2059798321002151
Maki-Yonekura, Saori et al. “Advances in cryo-EM and ED with a cold-field emission beam and energy filtration -Refinements of the CRYO ARM 300 system in RIKEN SPring-8 center.” Microscopy (Oxford, England) vol. 70,2 (2021): 232-240. doi:10.1093/jmicro/dfaa052
Sutherland, Hazel et al. “The Cryo-EM Structure of Vesivirus 2117 Highlights Functional Variations in Entry Pathways for Viruses in Different Clades of the Vesivirus Genus.” Journal of virology vol. 95,13 (2021): e0028221. doi:10.1128/JVI.00282-21
Hamaguchi, Tasuku et al. “Structure of the far-red light utilizing photosystem I of Acaryochloris marina.” Nature communications vol. 12,1 2333. 20 Apr. 2021, doi:10.1038/s41467-021-22502-8
Kato, Koji et al. “High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams.” Communications biology vol. 4,1 382. 22 Mar. 2021, doi:10.1038/s42003-021-01919-3
Çoruh, Orkun et al. “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster.” Communications biology vol. 4,1 304. 8 Mar. 2021, doi:10.1038/s42003-021-01808-9
Rennie, Martin L et al. “Structural basis of FANCD2 deubiquitination by USP1-UAF1.” Nature structural & molecular biology vol. 28,4 (2021): 356-364. doi:10.1038/s41594-021-00576-8
Ariyoshi, Mariko et al. “Cryo-EM structure of the CENP-A nucleosome in complex with phosphorylated CENP-C.” The EMBO journal vol. 40,5 (2021): e105671. doi:10.15252/embj.2020105671
Takaba, Kiyofumi et al. “Protein and Organic-Molecular Crystallography With 300kV Electrons on a Direct Electron Detector.” Frontiers in molecular biosciences vol. 7 612226. 6 Jan. 2021, doi:10.3389/fmolb.2020.612226
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Kishikawa, Jun-Ichi et al. “Mechanical inhibition of isolated Vo from V/A-ATPase for proton conductance.” eLife vol. 9 e56862. 8 Jul. 2020, doi:10.7554/eLife.56862
Fislage, Marcus et al. “Assessing the JEOL CRYO ARM 300 for high-throughput automated single-particle cryo-EM in a multiuser environment.” IUCrJ vol. 7,Pt 4 707-718. 11 Jun. 2020, doi:10.1107/S2052252520006065
Takaba, Kiyofumi et al. “Collecting large datasets of rotational electron diffraction with ParallEM and SerialEM.” Journal of structural biology vol. 211,2 (2020): 107549. doi:10.1016/j.jsb.2020.107549
Merk, Alan et al. “1.8 Å resolution structure of β-galactosidase with a 200 kV CRYO ARM electron microscope.” IUCrJ vol. 7,Pt 4 639-643. 11 Jun. 2020, doi:10.1107/S2052252520006855
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CRYO ARM Bibliography 2

Thu, 01 Oct 2026 15:27:47 GMT

Fujino M, Tanaka Y, Iwasaki W, Ito T, Yokoyama T, human 80S ribosome delta eL41 rotated state, To Be Published.
Voedts H, Nguyen PC, Nguyen VS, Leverrier P, Iorga BI, Cho SH, Remaut H, Collet JF, Stress-induced membrane insertion at the beta-barrel assembly machinery complex regulates BepA metalloprotease activity, Nat Commun (2026).
Fujino M, Tanaka Y, Iwasaki W, Ito T, Yokoyama T, human 80S ribosome delta eL41 non-rotated state, To Be Published.
Kohga H, Hosoda K, Tsukazaki T, JP Complex - E. coli MurJ, Levivirus PP7 lysis protein SglPP7, To Be Published.
Chong T, Rao G, Fu Y, Cao S, Fusion protein of Helicoverpa armigera nucleopolyhedrovirus in the uncleaved prefusion state, To Be Published.
Miyazaki R, Kohga H, Matsuoka N, Maruno Y, Yoshimoto W, Takahashi YS, Yanto DHY, Nugraha Y, Shigematsu H, Shiota T, Tsukazaki T, Cryo-EM structures of the SurA-BAM complex reveal conformational changes in outer membrane protein assembly., Nat Commun, 17 (2026).
Funahashi T, Yamaguchi H, Suzuki S, Suzuki H, Nishikawa K, Takahashi K, Tatsumi M, Mizukoshi T, Miyano H, Fujiyoshi Y, Sugiki M, Structural basis for substrate recognition in l-lysine 6-dehydrogenase from Geobacillus stearothermophilus by Cryo-EM., J Struct Biol, 218 (2026) 108366.
Fujino M, Tanaka Y, Iwasaki W, Ito T, Yokoyama T, human 80S ribosome non-rotated state, Nucleic Acids Res (2026).
Yoshida A, Yamamoto H, Miyata T, Tomita T, Yoshida M, Namba K, Kosono S, Kuzuyama T, Nishiyama M, Catalytic regulation of CoA transferase by an NAD -sensing accessory protein and protein acetylation, To Be Published.
Sonani R, Bodson T, Remaut H, Sleutel M, Protein polymers proliferate polymerization of proteases and phosphatases, To Be Published.
Imai H, Kanazawa R, Maeshima T, Tran DP, Shimo-Kon R, Tokita H, Miyata T, Makino F, Fujita J, Kato T, Kitao A, Namba K, Kon T, ADP-Bound States of Cytoplasmic Dynein: Cryo-electron Microscopy Reveals a Two-Step Post-Power-Stroke Transition and Roles of Regulatory ATPase Sites., J Mol Biol, 438 (2026) 169977.
Ichikawa K, Adachi T, Miyata T, Makino F, Namba K, Kitazumi Y, Shirai O, Sowa K, Structure-guided engineering of membrane-binding regions for surfactant-free solubilization of direct electron transfer-type alcohol dehydrogenase., Chem Commun, 62 (2026) 7948.
Feng Y, Qian GF, Dong XC, Structural basis of extracellular receptor assemblies mediated by IL-31, To Be Published.
Andries J, Toul M, Felix J, Clancy DM, Savvides SN, Structural basis of pro-inflammatory signaling via the IL-36 receptor mediated by IL-36g and IL-37, To Be Published.
Chong T, Rao G, Fu Y, Cao S, Fusion protein of Helicoverpa armigera nucleopolyhedrovirus in the postfusion state, To Be Published.
Jia H, Tang B, Liu S, Wen X, Wu F, Hu X, Zhou H, Chong T, Lv L, Liu Q, Rao G, Wei M, Jing X, Cao S, Deng F, Hu Z, Shu B, Gong R, Wu J, Wang M, Gong P, RNA synthesis and substrate analogue inhibition in the CCHFV polymerase., Nature (2026).
Chong T, Rao G, Fu Y, Cao S, Fusion protein of Helicoverpa armigera nucleopolyhedrovirus in the prefusion state, To Be Published.
Ludlam WG, Chang CT, Cechova K, Liauw BW, Cho HJ, Salar S, Sawh-Gopal A, Parvin A, Dhaliwal SK, Dhaliwal SK, Izard T, Bao H, Brown AM, Dunn HA, Vafabakhsh R, Martemyanov KA, Structural basis for modulation of group III mGlu receptors by transsynaptic interactions., Sci Adv, 12 (2026) eaed3793.
Khaja F, Antonyuk SV, Muench SP, Hsanain SS, Cryo-EM Structure of the N600A Quinol-Dependent Nitric Oxide Reductase, To Be Published.
Yamaguchi T, Minamino T, Kato T, Chevance FFV, Hughes KT, Namba K, Structural insights into the assembly mechanism of the molecular bushing in the bacterial flagellar motor., Commun Biol (2026).
Wang Z, Goto K, Tsugita A, Yokoyama T, Tanaka Y, Ogawa T, The Cryo-EM structure of Chum Salmon Oncorhynchus keta 24-mer lectin and Gb3 glycosphingolipid complex reveals a therapeutic potential for Alzheimer s disease, To Be Published.
Muraoka Y, Kobayashi S, Oskam L, Tateyama M, Masago A, Tanaka Y, Yokoyama T, Furuta T, Takase H, Tanudjaja E, Terashima S, Shimizukawa H, Yamanashi T, Saito S, Ijima H, Tanaka M, Miyamoto A, Kato M, Sato K, Tsujii M, Umezawa T, Quintero FJ, Rubio F, Kudla J, Ito M, Kubo Y, Ishimaru Y, Pierik R, Uozumi N, AKT5 is a bona fide potassium channel and controls petiole growth in Arabidopsis., Sci Adv, 12 (2026) eaeh7630.
Makino F, Yanagisawa H, Eisenstein F, Miyata T, Kinoshita M, Kikkawa M, Namba K, Subtomogram averaging by cryo electron tomography using CRYO ARM 300 II for purified and cellular samples, Aims Biophys, 13 (2026) 131.
Kato K, Nakajima Y, Shen JR, Nagao R, Structural basis for unique low-energy chlorophylls within photosystem I in Arthrospira platensis, To Be Published.
Wang M, Zhang X, Li W, Yao Y, Li E, Zhang B, Zhou J, Liu S, Gao Y, Zhu Z, Zhu L, Liu M, Hu J, Peng C, Li F, Chen M, Liu H, Yao C, Shang Y, Yan F, Gong P, Jin T, Chiu S, A highly potent nanobody-based bispecific therapeutic provides broad-spectrum protection against ebolavirus., Nat Commun, 17 (2026).
Suzuki S, Tran DP, Nishikawa K, Kitao A, Fujiyoshi Y, Mechanistic insight into signal bias by the agonist-dependent conformational dynamics of GPR84., Nat Commun, 17 (2026).
Shino Y, Muraki N, Kobatake Y, Kamishina H, Kosuge H, Nakakido M, Tsumoto K, Furukawa Y, Structural analysis of Cu/Zn-superoxide dismutase linked to neurodegenerative disease by antibody-guided cryo-EM., Protein Sci, 35 (2026) e70615.
Sleutel M, Sogues A, Gonzalez Socorro A, Cooman V, Fislage M, Nijhawan AK, Zuo X, Alva V, Remaut H, Conticello VP, Pyrodictium abyssi AbpX reveals a calcium-responsive family of microbial biomatrix proteins that form thermostable hydrogels., PNAS, 123 (2026) e2600204123.
Taguchi A, Fujita J, Tanabe M, Takaya D, Harada K, Moriya T, Fukuzawa K, Namba K, Nishino K, Structural insights into fosfomycin efflux by a streptococcal ABC transporter., PNAS, 123 (2026) e2535933123.
Tanaka Y, Nishigaya Y, Cryo-EM structure of RubisCO from Nitrosospira multiformis., Biochem Biophys Res Commun, 822 (2026) 153886.
Artigas P, Abe K, Passive aberrant currents are induced by all Na pump variants causing hypomagnesemia, To Be Published.
Artigas P, Abe K, On the mechanism of hypomagnesimia with treatment-resistant seizures cansed by variants of the Na,K -ATPase alpha1 subunit ATP1A1, To Be Published.
Yamori W, Nakazato I, Yuchen Q, Sanga Y, Miyata T, Uehara R, Noto Y, Namba K, Fukayama H, Matsumura H, Arimura S, CryoEM structure of Arabidopsis thaliana Col-0 Rubisco with D4 symmetry, To Be Published.
Suzuki S, Tanaka K, Nishikawa K, Fujiyoshi Y, Cryo-EM Structure of the Human Mas Receptor Reveals N-terminal Occlusion of the Orthosteric Ligand Binding Pocket., J Mol Biol, 438 (2026) 169844.
Yamori W, Nakazato I, Yuchen Q, Sanga Y, Miyata T, Uehara R, Noto Y, Namba K, Fukayama H, Matsumura H, Arimura S, CryoEM structure of Arabidopsis thaliana M309I Rubisco with D4 symmetry, To Be Published.
Tang J, Kuang W, Chen W, Wu H, Wang Y, Li J, Yuan Z, Xia H, Zhao H, Deng Z, Structural basis for RNA synthesis and inhibition of the orthobunyavirus polymerase., Nat Commun, 17 (2026).
Raoelijaona F, Szczepaniak J, Schahl A, Bray JE, Zhou JC, Baker L, El Omari K, Lowe E, Low YS, Rodriguez CM, Landsberg MJ, Lott JS, Kleanthous C, Chavent M, Maiden MC, Seiradake E, Ancestral neuronal receptors are bacterial accessory toxins., Nat Commun, 17 (2026).
Clancy DM, Sanz-Sanjuan A, Gilis E, Tougaard P, Velghe I, Van Droogenbroeck Y, Felix J, Bloch Y, Cuadrado AF, Merceron R, Schenck S, Vandenabeele P, Brunner JD, Taghon T, Elewaut D, Savvides SN, Structural and mechanistic insights into the constitutive Themis-Grb2 complex in T cell signalling., Nat Commun, 17 (2026).
Cai HL, Shimada A, Hamaguchi T, Mizoguchi A, Yonekura K, Tsuchiyama K, Shimada M, Ebihara A, Tani K, Nakagawa T, Cryo-EM Structures of Alcohol Oxidase Isozymes Reveal Structural Determinants of Cofactor Variation and Enzymatic Activity in Ogataea methanolica., Microb Biotechnol, 19 (2026) e70355.
Mima M, Sato K, Yokoyama T, Mishima-Tsumagari C, Ohnuki T, Tanaka Y, Iwamoto K, Cryo-EM elucidates the interaction mechanism of ozoralizumab, a humanized anti-TNF alpha NANOBODY 174; compound., Biochem Biophys Res Commun, 816 (2026) 153572.
Zhang S, Liu Y, Wu W, Liu Z, He Q, Wang T, Yang J, Yin H, Yuan Z, Zhang H, Allosteric activation mechanism of the type VII CRISPR-Cas system., Nucleic Acids Res, 54 (2026).
Tanaka K, Nishikawa K, Shiimura Y, Fujiyoshi Y, Tsutsumi N, Structural insights into biased signaling at chemokine receptor CCR7., PNAS, 123 (2026) e2533975123.
Oki H, Takebe K, Bonsu A, Fujii K, Masuda R, Henderson N, Mima T, Koide T, Moradi M, Matsushita O, Sakon J, Kawahara K, Bacterial collagenase harnesses collagen geometry for processive cleavage., Nat Commun, 17 (2026).
Baker RW, Kikkawa M, Sloan DE, Yanagisawa H, Structure of AP-2 bound to the dileucine motif and WxxPhi motif of CCDC32; consensus refinement, To Be Published.
Wang S, Rao G, Cao S, Gong R, A neutralizing antibody targeting the F protein of NiV, To Be Published.
Baker RW, Kikkawa M, Sloan DE, Yanagisawa H, Closed AP-2 clathrin adaptor complex in solution, To Be Published.
Wang S, Rao G, Cao S, Gong R, A broad-spectrum neutralizing antibody targeting the F protein of NiV and HeV, To Be Published.
Pradhan B, Kumar ST, Wagner J, Gallardo R, Orlando G, Vleeschouwer MD, Madine J, Louros N, Neher J, Schymkowitz J, Rousseau F, In Vitro Co-Aggregation with medin Induces an Abeta42-Like Polymorph of Abeta40 Fibrils., To Be Published.
Kleiz-Ferreira J, Brams M, Harrison PJ, Gallagher CI, Nys M, Donze Y, Quigley A, Bertrand D, Ulens C, Structure of a pH-sensitive pentameric ligand-gated ion channel from the Sarcoptes scabies mite., Nat Commun, 17 (2026).
Clairfeuille T, Rudolph M, Structures of N-methyl hydantoinase reveal large conformational changes during catalysis and a novel prototypic mechanism, To Be Published.
Liu Y, Liu B, Zhan W, Zhang L, Shi A, Lin L, Jiang M, Guo YR, Membrane dome-based regulation mechanism of the mechanosensitive PIEZO channel., Cell Rep, 44 (2025) 116651.
Sleutel M, Sogues A, Remaut H, Auto-crosslinking sporesilk fibers promote endospore and Cry toxin clustering.,UCSF ChimeraX: Structure visualization for researchers, educators, and developers, Protein Sci,Nat Commun, 17 (2026).
Gautam J, Wu J, Lally JSV, McNicol JD, Fayyazi R, Ahmadi E, Oniciu DC, Heaton S, Newton RS, Rehal S, Bhattacharya D, Di Pastena F, Nguyen B, Valvano CM, Townsend LK, Banskota S, Batchuluun B, Jabile MJT, Payne A, Lu J, Desjardins EM, Kubota N, Tsakiridis EE, Mistry B, Aganostopoulos A, Houde V, Dansercoer A, Verschueren KHG, Savvides SN, Hammill JA, Bezverbnaya K, Muti P, Tsakiridis T, Dai W, Jiang L, Hoshida Y, Larche M, Bramson JL, Friedman SL, Verstraete K, Wang D, Steinberg GR, ACLY inhibition promotes tumour immunity and suppresses liver cancer., Nature, 645 (2025) 507.
Drzazga AK, Suzuki S, Wouters C, Faas F, Nishikawa K, Kamegawa A, Fujiyoshi Y, Rosenkilde MM, Tsutsumi N, Activation of cytomegalovirus-encoded G protein-coupled receptor UL33 by an innate N-terminal peptide., Commun Biol, 9 (2026).
Gupta J, Le Coq J, Lietha D, Izard T, Structural insights into SHIP2 reveal its membrane regulatory mechanisms., Protein Sci, 35 (2026) e70479.
Kishida K, Kawakami K, Yonekura K, Arase H, Antigen-specific immune regulation mediated by self TCR-like antibodies, To Be Published.
Bazeli B, Shkumatov AV, Schenck S, Vanherck JC, Janssens A, Spieser SAH, Marchand D, Roelens R, Chaltin P, Marchand A, Vriens J, Voets T, Brunner JD, Stereoselectivity and functional plasticity of a common ligand-binding pocket in TRPM3., Nat Commun, 17 (2026).
Ishihara K, Matsumoto S, Gerle C, Gopalasingam CC, Shigematsu H, Shirai T, Numata T, Sequential structural rearrangements at the PAM-distal site of a type I-F3 CRISPR-Cas effector enabling RNA-guided DNA transposition., Nucleic Acids Res, 54 (2026).
Kano M, Kimura T, Yanagisawa H, Tatsumi L, Yamashita K, Sakai A, Li X, Saido TC, Saito T, Takatori S, Kikkawa M, Tomita T, Cryo-EM structure of pro-aggregant P301L/S320F double-mutant tau filaments formed in mouse brains following peripheral AAV delivery, bioRxiv (2026).
Uda K, Yamagami T, Ishino S, Gerle C, Gopalasingam CC, Shigematsu H, Numata T, Ishino Y, Substrate specificity and action mechanism of the HerA-NurA nuclease from the hyperthermophilic archaeon Thermococcus kodakarensis., Mbio, 17 (2026) e0352325.
Wang QQ, Ke XL, Li ET, Hong DX, Li HX, Cheng ZK, Zhang JC, Jin TC, Shu B, Chiu S, Cryo-EM structure of prefusion-stabilized RSV F DS-Cav1 strain: A2 in complex with nanobody 2A5, To Be Published.
Wang Y, Wu H, Li J, Tian Z, Deng Z, Cryo-EM structure of the bacterial anti-phage defense system DRT6., Biochem Biophys Res Commun, 791 (2025) 152955.
Zhang Y, Zhang Z, Yu F, Chen X, Yang S, Lin J, Liu G, Liu X, Guo M, Chen Y, Lan K, Zhao H, Broadly Sarbecovirus-Neutralizing Antibodies Induced by Ancestral SARS-CoV-2 Infection., Viruses, 17 (2025).
Wang QQ, Ke XL, Cryo-EM structure of prefusion-stabilized RSV F DS-Cav1 strain: A2 in complex with nanobody 1D8, To Be Published.
Umekubo N, Hashizume A, Saito H, Kato S, Kanai C, Gopalasingam CC, Gerle C, Shigematsu H, Yoshimori A, Abe K, Yokoshima S, Design, synthesis, and structural analysis of an inhibitor of the gastric proton pump with a diaza-tricyclic skeleton., Org.Biomol.Chem., 24 (2026) 1000.
Ke X, Shu B, cryo-EM density map of SFTSV virus complexed with with hA5-6 W30B/W53 Fab, To Be Published.
Borgini S, Pasveer E, Petre C, Iorga BI, Vertommen D, Remaut H, Collet JF, Lauber F, Identification of receptor-binding domains of Bacteroidales antibacterial pore-forming toxins., J Biol Chem, 302 (2025) 111113.
Ke X, Shu B, cryo-EM density map of SFTSV virus complexed with with hA5-6 W30B/W53 Fab, To Be Published.
Sakai R, Sato K, Tsugita A, Thaveepornkul L, Takada A, Miyamoto H, Kurokawa R, Yoshida M, Yokoyama T, Evidente A, Tsuge Y, Watari H, Sumiya T, Matumoto K, Chimnaronk S, Tanaka Y, Modulation of translational elongation by montanine alkaloids preferentially inhibits RNA viruses., bioRxiv (2025).
Ke X, Shu B, cryo-EM density map of SFTSV virus complexed with with hA5-6 W30B/W53 Fab, To Be Published.
Seki S, Litvin R, Bina D, Miyata T, Tanaka H, Namba K, Kurisu G, Polivka T, Fujii R, Cryo-EM structure of violaxanthin-chlorophyll a protein with red Chl: rVCP from Trachydiscus minutus., To Be Published.
Mishra BP, Loyo CL, Cai Y, Litfin T, Miraj G, Brillault L, Masic V, Mosaiab T, Rajaratnam P, Rudrawar S, Gu W, Kobe B, Gerdt JP, Grossman AD, Shi Y, Ve T, Molecular characterisation of the Bacillus subtilis SpbK antiphage defence system., Nat Commun, 17 (2025) 1051.
Soichiro S, Kubota M, Ishii A, Kim E, Tomoko M, Hideaki T, Keiichi N, Genji K, Minagawa J, Ritsuko F, Cryo-EM structure of the LHCp trimer from Ostreococcus tauri at 1.94 angstrom resolution, To Be Published.
Suzuki S, Kamegawa A, Kozai D, Nishikawa K, Irie K, Fujiyoshi Y, Cryo-EM structure of human AQP11 reveals a trimeric architecture with a large pore., Sci Adv, 12 (2026) eaeb5769.
Ouchi R, Numata T, A new in vitro reconstitution system of type III-B CRISPR-Cas effector for functional and structural studies, To Be Published.
Sassa M, Yamato H, Tanino H, Fukuda Y, Inoue T, Divergent acetyl-CoA binding modes mediate allosteric inhibition of bacterial hybrid-type malic enzymes., J Biol Chem, 301 (2025) 110887.
Inaoka D, Miyata T, Makino F, Ohtani Y, Ekari M, Kobayashi R, Imamura K, Sakamoto E, Kodama ST, Yoshida N, Kato T, Namba K, Tochio H, Sekiyama N, TIA-1 PLD amyloid fibril formation is suppressed by the ALS-associated mutation, To Be Published.
Zegeye ED, Sleutel M, Jonsmoen UL, Chen J, Morawska LP, Mekonnen YB, Kuipers OP, Remaut H, Aspholm M, Spatiotemporal expression of endospore appendages and cryo-EM insights into Ena1C-mediated S-ENA anchoring in Bacillus paranthracis.,UCSF ChimeraX: Structure visualization for researchers, educators, and developers,Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix, Acta Crystallogr D Struct Biol,Sci Rep,Protein Sci, 16 (2026) 7122.
Yan R, Wu M, Ge X, Jin Q, Wang M, Zhou H, Li Y, Wang Y, Yuan S, Strategic variations in sarbecovirus and merbecovirus Nsp1 linker regions for translation inhibition., Nucleic Acids Res, 54 (2026).
Qian Y, Gopalasingam CC, Gerle C, Shigematsu H, Abe K, Oshima A, Cryo-EM structure of the ATP11C Q79E mutant reveals the structural basis for altered Phospholipid recognition., J Biol Chem, 302 (2025) 110935.
Gupta J, Izard T, CryoEM structure of Rv2531c reveals cofactor-induced tetramer-dimer transition in a tuberculin amino acid decarboxylase., J Biol Chem, 301 (2025) 110394.
Ke X, Li X, Liu Z, Liu K, Liu W, Yan X, Shu B, Zhang C, Molecular mechanisms of receptor recognition and antibody neutralization of coxsackievirus A6., Nat Commun, 17 (2025) 934.
Zhou D, Wang Y, Yao Y, Kuang W, Cheng R, Zhang G, Liu H, Li X, Chiu S, Deng Z, Zhao H, Antigenic landscape of Nipah virus attachment glycoprotein analysis reveals a protective immunodominant epitope across species., NPJ Vaccines, 11 (2025) 5.
Eluru G, De Gieter S, Schenck S, Stroobants A, Shrestha B, Erbel P, Brunner JD, Efremov RG, MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony., Nat Methods, 22 (2025) 2563.
Yan R, Wu M, Ge X, Jin Q, Wang M, Zhou H, Li Y, Wang Y, Yuan S, Strategic variations in sarbecovirus and merbecovirus Nsp1 linker regions for translation inhibition., Nucleic Acids Res, 54 (2026).
Ke X, Li X, Liu Z, Liu K, Liu W, Yan X, Shu B, Zhang C, Molecular mechanisms of receptor recognition and antibody neutralization of coxsackievirus A6., Nat Commun, 17 (2025) 934.
Wang Y, Wu H, Li J, An Q, Tian Z, Deng Z, Anti-phage defense mechanism involving phage-encoded DNA binding protein and bacterial reverse transcriptase DRT4., Nat Commun, 17 (2025) 289.
Nakano A, Kishikawa JI, Yui N, Sugawara K, Kan Y, Gerle C, Shigematsu H, Mitsuoka K, Yokoyama K, Structures of rotary ATP synthase from Thermus thermophilus during proton powered ATP synthesis., Sci Adv, 11 (2025) eadx8771.
Tian K, Na H, Fu Y, Chong T, Leng C, Meng F, Liang Y, Wang M, Hu Z, Wang X, Rao G, Cao S, Structural polymorphism of two-dimensional lattices assembled from baculoviral capsid proteins., Virol Sin, 40 (2025) 935.
Kiss-Szeman AJ, Takacs L, Jakli I, Banoczi Z, Hosogi N, Traore DAK, Harmat V, Perczel A, Menyhard DK, Ligand binding Pro-miscuity of acylpeptide hydrolase, structural analysis of a detoxifying serine hydrolase., Protein Sci, 34 (2025) e70320.
Wang Y, Wu H, Sun J, Kuang W, Wang H, Ning YJ, Deng Z, Structural insight into RNA encapsidation by the severe fever with thrombocytopenia syndrome virus nucleocapsid protein., Mbio, 16 (2025) e0238125.
Takahashi YS, Kohga H, Chek MF, Yamamoto K, Takahashi JF, Shigematsu H, Tanaka Y, Ichikawa M, Miyazaki R, Hakoshima T, Tsukazaki T, Structural basis of a GatC ortholog transporter in the bacterial phosphotransferase system., FEBS Lett, 599 (2025) 2377.
Shibata S, Wang MY, Imasaki T, Shigematsu H, Ugarte La Torre D, Wei Y, Jobichen C, Hagio H, Sivaraman J, Sugita Y, Endow SA, Nitta R, Structural analysis of a motor with increased mechanical output reveals new transitions in kinesin microtubule motility.,Structural transitions in kinesin minus-end directed microtubule motility., Sci Rep,bioRxiv, 16 (2026) 487.
Waraich K, Meir A, Petrov F, Akbar S, Smith T, Anne Scott K, Dibben O, Bhella D, Structure of uncleaved Influenza A/Victoria/2570/2019 Haemagglutinin. The 2021 Influenza A H1N1 pdm09 egg-derived vaccine candidate., To Be Published.
Kato K, Nakajima Y, Sakamoto R, Kumazawa M, Ifuku K, Ishikawa T, Shen JR, Takabayashi A, Nagao R, Structural insights into the divergent evolution of a photosystem I supercomplex in Euglena gracilis., Sci Adv, 11 (2025) eaea6241.
Shibata S, Wang MY, Imasaki T, Shigematsu H, Wei Y, Jobichen C, Hagio H, Sivaraman J, Endow SA, Nitta R, Structural transitions in kinesin minus-end directed microtubule motility., bioRxiv (2024).
Sato K, Yokoyama T, Tanaka Y, Imaizumi R, Yasuda A, Yanai T, Yamashita S, Waki T, Tsunashima M, Nakayama T, Cryo-EM structure of chalcone synthase CHS from Physcomitrella patens in the presence of CHIL, To Be Published.
Liu M, Moody ERR, Blades F, Puente-Lelievre C, Chen KE, Stephens EJ, Michie KA, Cater RJ, Williams TA, Collins BM, Healy MD, The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking., Nat Commun, 17 (2026).
Peng R, Elkhaligy H, Grant T, Stagg SM, DiameTR: A cryo-EM tool for diameter sorting of tubular samples.,Structures of a FtsZ single protofilament and a double-helical tube in complex with a monobody., J Struct Biol X,Nat Commun, 12 (2025) 100136.
Li C, Efremov RG, Lipids modulate the open probability of RyR1 under cryo-EM conditions., Structure, 33 (2025) 2029.
Li C, Efremov RG, Primed-state RyR1 in 0.05 POPC micelles, in complex with a nanobody and FKBP, To Be Published.
Li C, Efremov RG, Open-state RyR1 in 0.05 POPC micelles, in complex with a nanobody and FKBP, To Be Published.
Li C, Efremov RG, Lipids modulate the open probability of RyR1 under cryo-EM conditions., Structure, 33 (2025) 2029.
Li C, Efremov RG, Open-state RyR1 in 0.01 POPC micelles, in complex with a nanobody and FKBP, To Be Published.
Li C, Efremov RG, transmembrane domain of Ryanodine receptor1, To Be Published.
Li C, Efremov RG, Primed-state RyR1 in 0.01 POPC micelles, in complex with a nanobody and FKBP, To Be Published.
Burton Smith RN, Murata K, Post-acquisition super resolution for cryo-electron microscopy., IUCrJ, 13 (2026) 589.
Kohga H, Lertpreedakorn N, Miyazaki R, Wu S, Hosoda K, Tanaka H, Takahashi YS, Yoshikaie K, Kuruma Y, Shigematsu H, Mori T, Tsukazaki T, Phage lysis protein Lys M acts as a wedge to block MurJ conformational changes., Sci Adv, 11 (2025) eady8083.
Bibby S, Jung J, Low YS, Amarilla AA, Newton ND, Scott CAP, Balk J, Ting YT, Freney ME, Liang B, Grant T, Coulibaly F, Young P, Hall RA, Hobson-Peters J, Modhiran N, Watterson D, A single residue in the yellow fever virus envelope protein modulates virion architecture and antigenicity., Nat Commun, 16 (2025) 8449.
Abe K, Marimuthu P, Qian Y, Gopalasingam CC, Gerle C, Shigematsu H, Tanaka K, Khandelia H, A unique gating mechanism revealed by the cryo-EM structure of monomeric ATP9A flippase., J Biol Chem, 301 (2025) 110631.
Maes L, Mares-Mejia I, Martin E, Bickel D, Claeys S, Vranken W, Fislage M, Galicia C, Versees W, Cryo-EM structures of the MnmE-MnmG complex reveal large conformational changes and provide new insights into the mechanism of tRNA modification., Nucleic Acids Res, 53 (2025).
Perez-Rafols A, Perez-Ropero G, Cerofolini L, Sperotto L, Roca-Martinez J, Higuera-Rodriguez RA, Russomanno P, Kaiser W, Vranken W, Danielson UH, Provenzani A, Martelli T, Sattler M, Buijs J, Fragai M, Deciphering the RNA recognition by Musashi-1 to design protein and RNA variants for in vitro and in vivo applications., Nucleic Acids Res, 53 (2025).
Han J, Liu B, Tang J, Zhang S, Wang X, Li X, Zhang Q, Liu Z, Wang W, Liu Y, Zhou R, Yin H, Wei Y, Li Z, Zhang M, Deng Z, Zhang H, Non-coding RNA mediates the defense-associated reverse transcriptase DRT anti-phage oligomerization transition., EMBO J, 44 (2025) 5429.
Wu HN, Fujita J, Nakura Y, Inoue M, Suzuki K, Ekimoto T, Yin B, Fukuda Y, Harada K, Inoue T, Ikeguchi M, Namba K, Yanagihara I, Structural Analysis and Molecular Dynamics Simulations of Urease From Ureaplasma parvum., J Mol Biol, 437 (2025) 169368.
Otsuki T, Matsumoto S, Fujita J, Miyata T, Namba K, Kanada R, Okuno Y, Kamada H, Ohno H, Akiba H, Conversion of an agonistic anti-TNFR2 biparatopic antibody into an antagonist by insertion of peptide linkers into the hinge region., J Biol Chem, 301 (2025) 110548.
Kinoshita M, Miyata T, Makino F, Imada K, Namba K, Minamino T, A beta-cap on the FliPQR protein-export channel acts as the cap for initial flagellar rod assembly., PNAS, 122 (2025) e2507221122.
Nanatani K, Kanno R, Kawabata T, Watanabe S, Hidaka M, Yamanaka T, Toda K, Fujiki T, Kunii K, Miyamoto A, Chiba F, Ogasawara S, Murata T, Humbel BM, Inaba K, Mitsuoka K, Guan L, Abe K, Yamamoto M, Koshiba S, Cryo-EM structure and molecular mechanism of the aspartate:alanine antiporter AspT from Tetragenococcus halophilus, To Be Published.
Adachi T, Ichikawa K, Miyata T, Makino F, Tanaka H, Namba K, Sowa K, Improved Direct Bioelectrochemical Fructose Oxidation with Surfactant-Free Heterotrimeric Fructose Dehydrogenase Variant Truncating Heme 1c and C-Terminal Hydrophobic Regions, ACS Electrochem (2025).
Minami A, Tanzawa T, Miyata T, Makino F, Yang Z, Funatsu T, Kuzuyama T, Yoshida H, Kato T, Ogawa T, Molecular basis of RNase I-mediated rRNA degradation regulated by ribosomes, bioRxiv (2025).
Fujita J, Kasai K, Hibino K, Kagoshima G, Kamimura N, Tobita S, Kato Y, Uehara R, Namba K, Uchihashi T, Matsumura H, Structural basis for the interaction between the bacterial cell division proteins FtsZ and ZapA., Nat Commun, 16 (2025) 5985.
Yamanashi T, Muraoka Y, Furuta T, Kume T, Sekido N, Saito S, Terashima S, Yokoyama T, Tanaka Y, Miyamoto A, Sato K, Ito T, Nakazawa H, Umetsu M, Tanudjaja E, Tsujii M, Dreyer I, Schroeder JI, Ishimaru Y, Uozumi N, Structure reveals a regulation mechanism of plant outward-rectifying K channel GORK by structural rearrangements in the CNBD-Ankyrin bridge., PNAS, 122 (2025) e2500070122.
Rodriguez Sarmiento RM, Berchtold S, Manevski N, Lindemann L, Dey F, Clairfeuille T, Amendola D, Vautrelle N, Duveau V, O Connor EC, Orally Bioavailable Dopamine D1/D5 Receptor-Biased Agonists to Study the Role of beta-Arrestin in Treatment-Related Dyskinesia in Parkinson s Disease., J Med Chem, 68 (2025) 13532.
Matthys A, Felix J, Catani JPP, Roose K, Nerinckx W, Van Buyten B, Fijalkowska D, Callewaert N, Savvides SN, Saelens X, Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses., Nat Commun, 16 (2025) 5831.
Hsi J, Mietzsch M, Patney M, Chen S, Sawh-Gopal A, Chipman P, McKenna R, Birds of a feather flock together: structural characterization of red-crowned crane and turkey aveparvoviruses., J Virol, 99 (2025) e0011025.
Yamaguchi T, Okatsu K, Kubota M, Mitsumori A, Yamagata A, Fukata Y, Fukata M, Shibata M, Fukai S, Structural insights into heterohexameric assembly of epilepsy-related ligand-receptor complex LGI1-ADAM22., eLife, 14 (2025).
Lambert F, Felix J, Wautier S, Dupre E, Jamez M, Michiels C, Gaignage M, Marien L, Lesage M, van der Woning B, Savvides SN, Lucas S, Antibody-mediated TGF-beta 1 activation for the treatment of diseases caused by deleterious T cell activity., Cell Rep, 44 (2025) 116061.
Imachi H, Nobu MK, Ishii S, Hirakata Y, Hashiguchi H, Hosogi N, Ikuta T, Isaji Y, Miyata M, Miyazaki M, Morono Y, Murata K, Nakagawa S, Narita A, Ogawara M, Okada S, Saito Y, Sakai S, Shimamura S, Tahara YO, Takaki Y, Takano Y, Tasumi E, Uemtatsu K, Yoshimura T, Takai K, Eukaryotes closest relatives are internally simple syntophic archaea., bioRxiv (2025).
Nomura R, Suzuki S, Nishikawa K, Suzuki H, Fujiyoshi Y, Structural insights into human adenylyl cyclase 9 in complex with G alpha s by cryo-EM., J Struct Biol, 217 (2025) 108223.
Isaacs A, Nieto GV, Zhang X, Modhiran N, Barr J, Thakur N, Low YS, Parry RH, Barnes JB, Jara R, Himelreichs J, Yao Y, Deride C, Barthou-Gatica B, Salinas-Rebolledo C, Ehrenfeld P, Hen JJ, Hayes N, Paramitha D, Morgan MS, McMillan CLD, Jones ML, Munro TP, Khromykh AA, Reading PC, Young PR, Chappell KJ, Shi Y, Bailey D, Marsh GA, Chiu S, Rojas-Fernandez A, Watterson D, A nanobody-based therapeutic targeting Nipah virus limits viral escape., Nat Struct Mol Biol, 32 (2025) 1920.
Sato K, Uehara S, Tsugita A, Ishii M, Ishiyama S, Maejima A, Nakahara I, Nazuka M, Matsui T, Christos G, Yokoyama T, Kumagai I, Makabe K, Asano R, Tanaka Y, Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement., Cell Rep, 44 (2025) 115965.
Kawahara K, Oki H, Iimori M, Muramoto R, Imai T, Gerle C, Shigematsu H, Matsuda S, Iida T, Nakamura S, High-resolution cryo-EM analysis visualizes hydrated type I and IV pilus structures from enterotoxigenic Escherichia coli., Structure, 33 (2025) 1040.
Wu M, Wan X, Zhou H, Yuan S, Flexibilities and conservations in the structural basis of viral -1 programmed ribosomal frameshifting, To Be Published.
Schenck S, Laeremans T, Steyaert J, Brunner JD, Structures of native SV2A reveal the binding mode for tetanus neurotoxin and anti-epileptic racetams., Nat Commun, 16 (2025) 4172.
Wu M, Wan X, Zhou H, Yuan S, Flexibilities and conservations in the structural basis of viral -1 programmed ribosomal frameshifting, To Be Published.
Wu B, Rao G, Zhang H, Yi Y, Zhao S, Qin Y, Li M, Chen L, Zhang Z, Zhang Z, Mu J, Chiu S, Cao S, Gong R, A C-based single-domain antibody broadly neutralizes SARS-CoV-2 and its variants through novel recognition of conserved regions in RBD, To Be Published.
Zhang Z, Chen G, 4-start helix structure of SBA/S3GN microtube with a diameter of about 32 nm, To Be Published.
Gopalasingam CC, Egami H, Shigematsu H, Sakaue M, Fukumoto K, Gerle C, Yamamoto M, Shiro Y, Muramoto K, Tosha T, Structural basis of Neisseria meningitidis quinol dependent nitric oxide reductase activation by dimerization., Commun Biol, 9 (2026).
Zhang Z, Cheng G, helix structure of SBA/S3GN microtube with a diameter of about 30 nm, To Be Published.
Monte D, Lens Z, Dewitte F, Fislage M, Aumercier M, Verger A, Villeret V, Structural basis of human Mediator recruitment by the phosphorylated transcription factor Elk-1., Nat Commun, 16 (2025) 3772.
Kato K, Kumazawa M, Nakajima Y, Suzuki T, Dohmae N, Shen JR, Ifuku K, Nagao R, Structure of a photosystem I supercomplex from Galdieria sulphuraria close to an ancestral red alga., Sci Adv, 11 (2025) eadv7488.
Gennaris A, Nguyen VS, Thouvenel L, Csoma N, Vertommen D, Iorga BI, Remaut H, Collet JF, Optimal functioning of the Lpt bridge depends on a ternary complex between the lipocalin YedD and the LptDE translocon., Cell Rep, 44 (2025) 115446.
Zmyslia M, Capper MJ, Grimmeisen M, Sartory K, Deuringer B, Abdelsalam M, Shen K, Jung M, Sippl W, Koch HG, Kaul L, Suss R, Kohnke J, Jessen-Trefzer C, A nanoengineered tandem nitroreductase: designing a robust prodrug-activating nanoreactor., Rsc Chem Biol, 6 (2024) 21.
Kasai K, Imamura K, Uno M, Nukui S, Sekiyama N, Miyata T, Makino F, Yamada R, Takahashi Y, Kodera N, Namba K, Ohnishi H, Narita A, Konno H, Tochio H, From Monomers to Oligomers: Structural Mechanism of Receptor-Triggered MyD88 Assembly in Innate Immune Signaling,Structural Mechanism of Receptor-Triggered MyD88 Oligomeric Assembly in Innate Immune Signaling., bioRxiv,Nat Commun (2026).
Kozai D, Inoue M, Suzuki S, Kamegawa A, Nishikawa K, Suzuki H, Ekimoto T, Ikeguchi M, Fujiyoshi Y, Narrowed pore conformations of aquaglyceroporins AQP3 and GlpF., Nat Commun, 16 (2025) 2653.
Isozaki Y, Makikawa T, Kimura K, Nishihara D, Fujino M, Tanaka Y, Hayashi C, Ishizaki Y, Igarashi M, Yokoyama T, Toshima K, Takahashi D, Creation of a macrolide antibiotic against non-tuberculous Mycobacterium using late-stage boron-mediated aglycon delivery., Sci Adv, 11 (2025) eadt2352.
Xu M, Zhang Z, Sun Y, Mai H, Liu S, Liu S, Lv K, Yu F, Wang Y, Yue X, Zhang J, Cai X, Zhao R, Lu H, Liu L, Luo H, Zhao H, Wang Y, Gong P, Chen S, Jing X, Zhao J, Chen YQ, IgA class switching enhances neutralizing potency against SARS-CoV-2 by increased antibody hinge flexibility., Antiviral Res, 235 (2025) 106082.
Sleutel M, Sogues A, Van Gerven N, Jonsmoen UL, Van Molle I, Fislage M, Theunissen LD, Bellis NF, Baquero DP, Egelman EH, Krupovic M, Wang F, Aspholm M, Remaut H, Cryo-EM analysis of the Bacillus thuringiensis extrasporal matrix identifies F-ENA as a widespread family of endospore appendages across the Firmicutes phylum.,Cryo-EM identifies F-ENA of Bacillus thuringiensis as a widespread family of endospore appendages across Firmicutes., bioRxiv,Nat Commun, 16 (2025) 7652.
Toyonaga T, Kato T, Kawamoto A, Miyata T, Kawakami K, Fujita J, Hamaguchi T, Namba K, Miyata M, Dimeric assembly of F 1 -like ATPase for the gliding motility of Mycoplasma., Sci Adv, 11 (2025) eadr9319.
Vizarraga D, Kawamoto A, Marcos-Silva M, Martin J, Makino F, Miyata T, Roel-Touris J, Marcos E, Pich OQ, Aparicio D, Fita I, Miyata M, Pinol J, Namba K, Kenri T, Dynamics of the adhesion complex of the human pathogens Mycoplasma pneumoniae and Mycoplasma genitalium., PLoS Pathog, 21 (2025) e1012973.
Yamaguchi H, Kitajima S, Suzuki H, Suzuki S, Nishikawa K, Kamegawa A, Fujiyoshi Y, Takahashi K, Tagami U, Maruyama Y, Kuroda M, Sugiki M, Cryo-EM structure of the calcium-sensing receptor complexed with the kokumi substance gamma-glutamyl-valyl-glycine., Sci Rep, 15 (2025) 3894.
Ma CB, Liu C, Park YJ, Tang J, Chen J, Xiong Q, Lee J, Stewart C, Asarnow D, Brown J, Tortorici MA, Yang X, Sun YH, Chen YM, Yu X, Si JY, Liu P, Tong F, Huang ML, Li J, Shi ZL, Deng Z, Veesler D, Yan H, Multiple independent acquisitions of ACE2 usage in MERS-related coronaviruses., Cell, 188 (2025) 1693.
Kawamoto A, Vizarraga D, Marcos-Silva M, Martin J, Makino F, Miyata T, Roel J, Marcos E, Aparicio D, Fita I, Miyata M, Pinol J, Namba K, Kenri T, Antibodies halting motility in Mycoplasma pneumoniae reveal the dynamic nature of the adhesion complex, bioRxiv (2023).
Nanatani K, Kanno R, Kawabata T, Watanabe S, Hidaka M, Yamanaka T, Toda K, Fujiki T, Kunii K, Miyamoto A, Chiba F, Ogasawara S, Murata T, Humbel BM, Inaba K, Mitsuoka K, Guan L, Abe K, Yamamoto M, Koshiba S, Cryo-EM structure and molecular mechanism of the aspartate:alanine antiporter AspT from Tetragenococcus halophilus, To Be Published.
Ye L, Dong X, Wang C, Lin Y, Lee MS, Li L, Chen G, Helical protein nanotubules assembled from sacrificial supramolecular polymers., Nat Synth (2025).
Nakamura S, Tanimura Y, Nomura R, Suzuki H, Nishikawa K, Kamegawa A, Numoto N, Tanaka A, Kawabata S, Sakaguchi S, Emi A, Suzuki Y, Fujiyoshi Y, Structure-guided engineering of a mutation-tolerant inhibitor peptide against variable SARS-CoV-2 spikes., PNAS, 122 (2025) e2413465122.
Suzuki S, Tanaka K, Kamegawa A, Nishikawa K, Suzuki H, Oshima A, Fujiyoshi Y, Structural insights into the engagement of lysophosphatidic acid receptor 1 with different G proteins., J Struct Biol, 217 (2024) 108164.
Kinoshita M, Makino F, Miyata T, Imada K, Namba K, Minamino T, Structural basis for assembly and function of the Salmonella flagellar MS-ring with three different symmetries., Commun Biol, 8 (2025) 61.
Hu H, Leng C, Shu Y, Peng L, Wu F, Liu J, Zhang X, Zhou W, Xiao Q, Li Y, Wu B, Shen J, Li J, Gong R, Yan B, Deng F, Hu Z, Cao S, Wang M, Structural insights into hybridoma-derived neutralizing monoclonal antibodies against Omicron BA.5 and XBB.1.16 variants of SARS-CoV-2., J Virol, 99 (2025) e0130724.
Li C, Willegems K, Uchanski T, Pardon E, Steyaert J, Efremov RG, Rapid small-scale nanobody-assisted purification of ryanodine receptors for cryo-EM., J Biol Chem, 300 (2024) 107734.
Sleutel M, Sonani RR, Miller JG, Wang F, Gonzalez Socorro A, Chen Y, Martin R, Demeler B, Rudolph MJ, Alva V, Remaut H, Egelman EH, Conticello VP, Donor strand complementation and calcium ion coordination drive the chaperone-free polymerization of archaeal cannulae.,Donor Strand Complementation and Calcium Ion Coordination Drive the Chaperone-free Polymerization of Archaeal Cannulae., bioRxiv,Nat Commun, 16 (2025) 9082.
Chen M, Jin Q, Zhang K, Wang Y, Chen H, Yu Z, Matthews S, Yuan S, Liu B, A phage encoded sigA-dependent transcription inhibitor also attacks host HelD-mediated defence system, To Be Published.
Jia X, Jing X, Li M, Gao M, Zhong Y, Li E, Liu Y, Li R, Yao G, Liu Q, Zhou M, Hou Y, An L, Hong Y, Li S, Zhang J, Wang W, Zhang K, Gong P, Chiu S, An adenosine analog shows high antiviral potency against coronavirus and arenavirus mainly through an unusual base pairing mode., Nat Commun, 15 (2024) 10750.
Abe K, McDermott J, Valia Madapally H, Marimuthu P, Gopalasingam CC, Gerle C, Shigematsu H, Khandelia H, Blanco G, Molecular Structure of the Na ,K -ATPase alpha 4 beta 1 Isoform in Its Ouabain-Bound Conformation., Int J Mol Sci, 25 (2024).
Lewis CB, Sherry L, Conley MJ, Nakashima M, Akbar S, Govindan N, Hosie MJ, Bhella D, Conformational Flexibility in Capsids Encoded by the Caliciviridae ., Viruses, 16 (2024).
Chen M, Jin Q, Zhang K, Wang Y, Chen H, Yu Z, Matthews S, Yuan S, Liu B, A phage encoded sigA-dependent transcription inhibitor also attacks host HelD-mediated defence system, To Be Published.
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R, Structure-based validation of recombinant light-harvesting complex II., Pnas Nexus, 3 (2024) pgae405.
Yang M, Rao G, Li L, Qi L, Ma C, Zhang H, Gong J, Wei B, Zhang XE, Chen G, Cao S, Li F, Transformation of a Viral Capsid from Nanocages to Nanotubes and Then to Hydrogels: Redirected Self-Assembly and Effects on Immunogenicity., ACS Nano, 18 (2024) 13755.
Kato K, Nakajima Y, Xing J, Kumazawa M, Ogawa H, Shen JR, Ifuku K, Nagao R, Structural basis for molecular assembly of fucoxanthin chlorophyll a / c -binding proteins in a diatom photosystem I supercomplex., eLife, 13 (2024).
Yanagisawa H, Arai H, Wang T, Miyazawa H, Kikkawa M, Oda T, Cryo-EM of wild-type and mutant PMEL amyloid cores reveals structural mechanism of pigment dispersion syndrome., Nat Commun, 16 (2025) 5411.
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Kasai K, Imamura K, Uno M, Nukui S, Sekiyama N, Miyata T, Makino F, Yamada R, Takahashi Y, Kodera N, Namba K, Ohnishi H, Narita A, Konno H, Tochio H, From Monomers to Oligomers: Structural Mechanism of Receptor-Triggered MyD88 Assembly in Innate Immune Signaling,Structural Mechanism of Receptor-Triggered MyD88 Oligomeric Assembly in Innate Immune Signaling., bioRxiv,Nat Commun (2026).
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Waraich K, Makino F, Miyata T, Kinoshita M, Minamino T, Namba K, Salmonella enterica serovar Typhimurium FliC G426A delta 204-292 forming the L-type straight filament, To Be Published.
Spagnolo L, Aspinall L, CryoEM structure of PhiC31 integrase on DNA, To Be Published.
Ishii Y, Naito K, Yokoyama T, Tanaka Y, Matsuura T, alpha-Hemolysin G122S/K147R -SpyTag/SpyCatcher head to head 14-mer, To Be Published.
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Fukawa E, Suzuki Y, Adachi T, Miyata T, Makino F, Tanaka H, Namba K, Sowa K, Kitazumi Y, Shirai O, Structural and electrochemical elucidation of biocatalytic mechanisms in direct electron transfer-type D-fructose dehydrogenase., Electrochim Acta, 490 (2024).
Galicia C, Guaitoli G, Fislage M, Gloeckner CJ, Versees W, Structural insights into the GTP-driven monomerization and activation of a bacterial LRRK2 homolog using allosteric nanobodies.,Structural insights in the GTP-driven monomerization and activation of a bacterial LRRK2 homologue using allosteric nanobodies, eLife, 13 (2024).
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Ishimaru H, Nishimura M, Shigematsu H, Marini MI, Hasegawa N, Takamiya R, Iwata S, Mori Y, Epitopes of an antibody that neutralizes a wide range of SARS-CoV-2 variants in a conserved subdomain 1 of the spike protein., J Virol, 98 (2024) e0041624.
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Li Z, Xia H, Rao G, Fu Y, Chong T, Tian K, Yuan Z, Cao S, Cryo-EM structures of Banna virus in multiple states reveal stepwise detachment of viral spikes., Nat Commun, 15 (2024) 2284.
Liao Z, Gopalasingam CC, Kameya M, Gerle C, Shigematsu H, Ishii M, Arakawa T, Fushinobu S, Structural insights into thermophilic chaperonin complexes., Structure, 32 (2024) 679.
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Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L, Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted., Ebiomedicine, 100 (2024) 104960.
Li L, Chong T, Peng L, Liu Y, Rao G, Fu Y, Shu Y, Shen J, Xiao Q, Liu J, Li J, Deng F, Yan B, Hu Z, Cao S, Wang M, Neutralizing monoclonal antibodies against the Gc fusion loop region of Crimean-Congo hemorrhagic fever virus., PLoS Pathog, 20 (2024) e1011948.
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Suzuki Y, Makino F, Miyata T, Tanaka H, Namba K, Kano K, Sowa K, Kitazumi Y, Shirai O, Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry., ACS Catal, 13 (2023).
Akiba H, Fujita J, Ise T, Nishiyama K, Miyata T, Kato T, Namba K, Ohno H, Kamada H, Nagata S, Tsumoto K, Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection., Commun Biol, 6 (2023) 987.
Liu Q, Zhao H, Li Z, Zhang Z, Huang R, Gu M, Zhuang K, Xiong Q, Chen X, Yu W, Qian S, Zhang Y, Tan X, Zhang M, Yu F, Guo M, Huang Z, Wang X, Xiang W, Wu B, Mei F, Cai K, Zhou L, Zhou L, Wu Y, Yan H, Cao S, Lan K, Chen Y, Broadly neutralizing antibodies derived from the earliest COVID-19 convalescents protect mice from SARS-CoV-2 variants challenge., Signal Transduct Target Ther, 8 (2023) 347.
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Suzuki S, Tanaka K, Nishikawa K, Suzuki H, Oshima A, Fujiyoshi Y, Structural basis of hydroxycarboxylic acid receptor signaling mechanisms through ligand binding., Nat Commun, 14 (2023) 5899.
Yang S, Wang Y, Yu F, Cheng R, Zhang Y, Zhou D, Ren X, Deng Z, Zhao H, Structural and functional insights into the modulation of T cell costimulation by monkeypox virus protein M2., Nat Commun, 14 (2023) 5186.
Abe K, Ozako M, Inukai M, Matsuyuki Y, Kitayama S, Kanai C, Nagai C, Gopalasingam CC, Gerle C, Shigematsu H, Umekubo N, Yokoshima S, Yoshimori A, Deep learning driven de novo drug design based on gastric proton pump structures., Commun Biol, 6 (2023) 956.
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Imai S, Suzuki H, Fujiyoshi Y, Shimada I, Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor., Nat Commun, 14 (2023) 4977.
Fujita J, Amesaka H, Yoshizawa T, Hibino K, Kamimura N, Kuroda N, Konishi T, Kato Y, Hara M, Inoue T, Namba K, Tanaka SI, Matsumura H, Structures of a FtsZ single protofilament and a double-helical tube in complex with a monobody., Nat Commun, 14 (2023) 4073.
Adachi T, Miyata T, Makino F, Tanaka H, Namba K, Kano K, Sowa K, Kitazumi Y, Shirai O, Experimental and Theoretical Insights into Bienzymatic Cascade for Mediatorless Bioelectrochemical Ethanol Oxidation with Alcohol and Aldehyde Dehydrogenases, ACS Catal, 13 (2023) 7955.
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Tsirigotaki A, Dansercoer A, Verschueren KHG, Markovic I, Pollmann C, Hafer M, Felix J, Birck C, Van Putte W, Catteeuw D, Tavernier J, Fernando Bazan J, Piehler J, Savvides SN, Verstraete K, Mechanism of receptor assembly via the pleiotropic adipokine Leptin., Nat Struct Mol Biol, 30 (2023) 551.
Chen Z, Watanabe S, Hashida H, Inoue M, Daigaku Y, Kikkawa M, Inaba K, Cryo-EM structures of human SPCA1a reveal the mechanism of Ca 2 /Mn 2 transport into the Golgi apparatus., Sci Adv, 9 (2023) eadd9742.
Himiyama T, Hamaguchi T, Yonekura K, Nakamura T, Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins., Bioconjug.Chem. (2023).
Schwefel D, Cryo-EM structure of SARS-CoV-2 spike Omicron BA.1 variant in complex with nanobody W25 map 4, one RBD up, To Be Published.
Modhiran N, Lauer SM, Amarilla AA, Hewins P, Lopes van den Broek SI, Low YS, Thakur N, Liang B, Nieto GV, Jung J, Paramitha D, Isaacs A, Sng JDJ, Song D, Jorgensen JT, Cheuquemilla Y, Burger J, Andersen IV, Himelreichs J, Jara R, MacLoughlin R, Miranda-Chacon Z, Chana-Cuevas P, Kramer V, Spahn C, Mielke T, Khromykh AA, Munro T, Jones ML, Young PR, Chappell K, Bailey D, Kjaer A, Herth MM, Jurado KA, Schwefel D, Rojas-Fernandez A, Watterson D, A nanobody recognizes a unique conserved epitope and potently neutralizes SARS-CoV-2 omicron variants., iScience, 26 (2023) 107085.
Nagao R, Kato K, Hamaguchi T, Ueno Y, Tsuboshita N, Shimizu S, Furutani M, Ehira S, Nakajima Y, Kawakami K, Suzuki T, Dohmae N, Akimoto S, Yonekura K, Shen JR, Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120., Nat Commun, 14 (2023) 920.
Dupuy E, Van der Verren SE, Lin J, Wilson MA, Dachsbeck AV, Viela F, Latour E, Gennaris A, Vertommen D, Dufrene YF, Iorga BI, Goemans CV, Remaut H, Collet JF, A molecular device for the redox quality control of GroEL/ES substrates., Cell, 186 (2023) 1039.
Wakabayashi T, Oide M, Kato T, Nakasako M, Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy., FEBS J, 290 (2023) 5514.
Suzuki Y, Makino F, Miyata T, Tanaka H, Namba K, Kano K, Sowa K, Kitazumi Y, Shirai O, Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry, ACS Catal, 13 (2023) 13828.
Bhella D, Love AJ, Streetley J, Taliansky M, McGeachy K, Bukharova T, 1.85 angstrom resolution cryo-EM reconstruction of tobacco mosaic virus, imaged on a JEOL CryoARM 300 with Direct Electron Apollo camera., To Be Published.
Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K, Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding., J Biol Chem, 299 (2023) 102884.
Sakaniwa K, Fujimura A, Shibata T, Shigematsu H, Ekimoto T, Yamamoto M, Ikeguchi M, Miyake K, Ohto U, Shimizu T, TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction., Nat Commun, 14 (2023) 164.
Yin J, Fu Y, Rao G, Li Z, Tian K, Chong T, Kuang K, Wang M, Hu Z, Cao S, Structural transitions during the cooperative assembly of baculovirus single-stranded DNA-binding protein on ssDNA., Nucleic Acids Res, 50 (2022) 13100.
Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K, Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding., J Biol Chem, 299 (2023) 102884.
Rangarajan ES, Smith EW, Izard T, The nematode alpha-catenin ortholog, HMP1, has an extended alpha-helix when bound to actin filaments., J Biol Chem, 299 (2022) 102817.
Wang X, Yu G, Wen Y, An Q, Li X, Liao F, Lian C, Zhang K, Yin H, Wei Y, Deng Z, Zhang H, Target RNA-guided protease activity in type III-E CRISPR-Cas system., Nucleic Acids Res, 50 (2022) 12913.
Suzuki Y, Makino F, Miyata T, Tanaka H, Namba K, Kano K, Sowa K, Kitazumi Y, Shirai O, Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry, ACS Catal, 13 (2023) 13828.
Otsubo R, Minamitani T, Kobiyama K, Fujita J, Ito T, Ueno S, Anzai I, Tanino H, Aoyama H, Matsuura Y, Namba K, Imadome KI, Ishii KJ, Tsumoto K, Kamitani W, Yasui T, Human antibody recognition and neutralization mode on the NTD and RBD domains of SARS-CoV-2 spike protein., Sci Rep, 12 (2022) 20120.
Hamaguchi T, Yonekura K, Cryo-EM structure of Beta-galactosidase at 1.57A resolution, To Be Published.
Yu G, Wang X, Zhang Y, An Q, Wen Y, Li X, Yin H, Deng Z, Zhang H, Structure and function of a bacterial type III-E CRISPR-Cas7-11 complex., Nat Microbiol, 7 (2022) 2078.
Lemonidis K, Rennie ML, Arkinson C, Chaugule VK, Clarke M, Streetley J, Walden H, Structural and biochemical basis of interdependent FANCI-FANCD2 ubiquitination., EMBO J, 42 (2023) e111898.
Yu G, Wang X, Zhang Y, An Q, Wen Y, Li X, Yin H, Deng Z, Zhang H, Structure and function of a bacterial type III-E CRISPR-Cas7-11 complex., Nat Microbiol, 7 (2022) 2078.
Fujita J, Makino F, Asahara H, Moriguchi M, Kumano S, Anzai I, Kishikawa JI, Matsuura Y, Kato T, Namba K, Inoue T, Epoxidized graphene grid for highly efficient high-resolution cryoEM structural analysis., Sci Rep, 13 (2023) 2279.
Shkumatov AV, Aryanpour N, Oger CA, Goossens G, Hallet BF, Efremov RG, Structural insight into Tn3 family transposition mechanism., Nat Commun, 13 (2022) 6155.
Haney J, Vijayakrishnan S, Streetley J, Dee K, Goldfarb DM, Clarke M, Mullin M, Carter SD, Bhella D, Murcia PR, Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles., Nat Microbiol, 7 (2022) 1879.
Nakano A, Kishikawa JI, Nakanishi A, Mitsuoka K, Yokoyama K, Structural basis of unisite catalysis of bacterial F 0 F 1 -ATPase., Pnas Nexus, 1 (2022) pgac116.
Li J, Hamaoka N, Makino F, Kawamoto A, Lin Y, Rogner M, Nowaczyk MM, Lee YH, Namba K, Gerle C, Kurisu G, Structure of cyanobacterial photosystem I complexed with ferredoxin at 1.97 angstrom resolution., Commun Biol, 5 (2022) 951.
Manik MK, Shi Y, Li S, Zaydman MA, Damaraju N, Eastman S, Smith TG, Gu W, Masic V, Mosaiab T, Weagley JS, Hancock SJ, Vasquez E, Hartley-Tassell L, Kargios N, Maruta N, Lim BYJ, Burdett H, Landsberg MJ, Schembri MA, Prokes I, Song L, Grant M, DiAntonio A, Nanson JD, Guo M, Milbrandt J, Ve T, Kobe B, Cyclic ADP ribose isomers: Production, chemical structures, and immune signaling., Science, 377 (2022) eadc8969.
Janssens A, Nguyen VS, Cecil AJ, Van der Verren SE, Timmerman E, Deghelt M, Pak AJ, Collet JF, Impens F, Remaut H, SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains, Nature (2023).
Maeda R, Fujita J, Konishi Y, Kazuma Y, Yamazaki H, Anzai I, Watanabe T, Yamaguchi K, Kasai K, Nagata K, Yamaoka Y, Miyakawa K, Ryo A, Shirakawa K, Sato K, Makino F, Matsuura Y, Inoue T, Imura A, Namba K, Takaori-Kondo A, A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron., Commun Biol, 5 (2022) 669.
Bammes B, Spilman M, Sakamoto M, Fukumura T, Konyuba Y, Okunishi E, Apoferritin structure at 1.46 angstrom resolution by CryoARM300 equipped with Apollo, To Be Published.
Kishikawa J, Nakanishi A, Nakano A, Saeki S, Furuta A, Kato T, Mistuoka K, Yokoyama K, Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases., Nat Commun, 13 (2022) 1213.
Jiang H, Ariyoshi M, Watanabe R, Makino F, Namba K, Fukagawa T, The cryo-EM structure of the CENP-A nucleosome in complex with ggKNL2., bioRxiv (2022).
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CRYO ARM™ series microscopes for cryo-EM in structural analysis of proteins and viruses

Wed, 02 Feb 2022 09:20:47 GMT

Introduction

Cryo-EM has seen an enormous increase in capabilities and potential in recent years owing to a number of technological advances, e.g. direct detector devices and improved scope automation. JEOL released two electron cryo-microscopes in 2017 specifically designed for automated and unattended, continuous operation at 200 and 300 kV, the CRYO ARM™ series. A recent update on both type of CRYO ARMs has the potential of increasing the throughput well beyond the current limit of 20,000 images/day, namely north of 50,000 images/day as well as extending the resolution to nearly true atomic resolution, i.e. 1.2Å.

Minimum Fringe Illumination and Aberration Free Image Shift

In order to increase the throughput to current levels two techniques have been critically important. One is the reduction of Fresnel fringes from the CL apertures when matching the beam diameter to the field of view of the camera. JEOL has introduced Köhler illumination on the CRYO ARM series microscopes to achieve this (Fig. 1). For the CRYO ARM™ 200 this results in Minimum Fringe Illumination, whereas on the CRYO ARM™ 300 this is implemented as Zero-Fringe Illumination. The second technique is the implementation of the Aberration Free Image Shift, where a narrow parallel beam gets steered inside the hole of a Quantifoil specimen using beam shift and image shift. This approach can be extended to cover multiple adjacent holes with an optional coma correction. (Fig. 1).

Fig. 1: Minimum (or Zero) Fringe Illumination implemented on the JEOL CRYO ARM™ series electron cryo-microscopes. Using Köhler illumination the Fresnel fringes arising from the CL apertures (left) can minimized allowing the beam diameter to be matched to the field of view of the detector without sacrificing usable area (middle left). Using beam shift and image shift with an optional correction for coma, the narrow, parallel beam can be steered inside a Quantifoil hole to create an intra-hole multi-record (middle right). Extending this to adjacent creates the inter-hole multi-record, here depicted as a 7x7x8 pattern (right).

Long-term stability

To enable long running imaging sessions two other areas were improved, i.e. stability of the Cold Field Emission gun (CFEG) and the Omega-style in-column energy filter. The CFEG requires periodic flashing to reset the emission to 100%. The second-generation CFEG can now operate for an entire day without requiring this (Fig. 2). If flashing is needed, remote control software will interrupt the imaging run, flash the tip and continue, a process which takes < 1 min. No adjustment of coma is required. The stability of the energy filter has also been dramatically improved. Both these improvements not only dramatically increase run times for imaging, but also minimize the amount of time users need to spend with the microscope resulting in better throughput. Finally, tuning of the Omega filter is now done automatically.

Fig. 2: Improvement of the CFEG reveals minimal requirements for flashing the tip (left). The Omega-style energy filter now shows minimal drift of the Zero Loss peak (right).

Interoperability

In order to optimize inter-operability between JEOL and other brands of cryo microscopes it is imperative to be able to transfer frozen-hydrated grids between microscopes. From fig. 3 we can glean that reverse transfers work. Minimal ice contamination is present on the sample after the reverse and subsequent second cryo-transfer.

Fig. 3: Results after first cryo-transfer (left) and after a reverse and subsequent cryo-transfer into a CRYO ARM 300 II (right). Minimal ice contamination accumulates during the second transfer.

Figure 4 shows the main cartridges used in the CRYO ARM™ series electron cryo-microscopes for imaging in SPA workflows and single-axis tomography. For complete inter-operability with non-JEOL brand cryo-microscopes JEOL have developed a cartridge that is compatible with AG-clipped grids (Fig. 4). Whereas the standard cartridge uses a c-clip to secure the grid, the AG-cartridge employs a sliding cover.

Fig. 4: Standard cartridges for the CRYO ARM™ series microscopes (left) and the AG-compatible cartridges (right).

Figure 5 shows results obtained from apo-ferritin using an AG-compatible cartridge after only 30 minutes of data collection. The grid square image does not show significantly larger amounts of ice-contamination. The 3D map was obtained using only 150 micrographs and from the FSC curve can be seen to have a resolution of 2Å.

Fig. 5: Results from apo-ferritin sample in an AG-compatible cartridge.

Throughput challenge I

Figure 6 shows results from an experiment attempted to determine how much data is needed to break 1.5Å resolution using apo-ferritin mounted in a standard cartridge. On the CRYO ARM™ 300 II this took only a half hour of data collection. In fact, the core of the particle shows a resolution of better than 1.5Å strongly suggesting that a well-behaved sample can yield usable data in about an hour. Whereas elsewhere it has been suggested that screening ought to be done using a dedicated tool, these results suggest that not only can screening be done effectively on a CRYO ARM™ 300 II -note that sample transfer and retrieval does NOT affect already loaded samples - but these results also give a clear indication how well behaved the sample is and thus a good indication how far the data can be pushed.

Fig. 6: Results from apo-ferritin obtained to determine the amount of data/time needed to break 1.5Å. The results were obtained after only 30 minutes.

Throughput challenge II

Figure 7 shows results from pushing the data collection and processing as far as it would go within reasonable time frames. A total of 7500 micrographs were collected from which 500,000 particles were selected. Processing yielded a 1.29Å close to the limits discussed by Yip et al. (Nature 587 (2020) 157. The CFEG clearly gives data that is extremely close to be officially called atomic resolution, but in a standard package in for a price considerably less than the other-brand cryo-microscopes.
Final note: all the data collection is done using serialEM employing a multi-record scheme with a 5x5x4 pattern imaged on a K3 camera.

Fig. 7: Results from apo-ferritin sample. Final map is at 1.29Å resolution.

Teaser

Ask us about our CRYO ARM™ 200 II electron cryo-microscope. Also, ask us about our uptime guarantee.

The JEOL CRYO ARM™ series electron cryo-microscopes enable researchers to get fast results.
The JEOL CRYO ARM™ series electron cryo-microscopes allow researchers to get nearly atomic resolution data.
The JEOL CRYO ARM™ series enjoys impressively robust usage times of more than a year with single interruption.

Jaap Brink¹, Taku Fukumura¹, Tom Isabell¹, Sohei Motoki², Isamu Ishikawa², Yoshi Okhura²
¹JEOL USA, Inc., Peabody, 01960 MA. USA, ²JEOL Ltd, 3-1-2 Musashino, Akishima, Tokyo 196-8558, JAPAN

CryoNote

Sun, 13 Feb 2022 17:08:15 GMT

“Visualize the truth” is a hope of researchers who use various measuring equipment. Researchers who use electron microscopes as well have a desire to observe the real structure.

But actually, in experiments using electron microscopes, many problems arise: They include damage regions of the specimen when it is cut for the size suited to observation, artifacts due to the staining that is applied to enhance image contrast, deformation caused by substitution of water to resin for withstanding vacuum exposure, and thermal damage to the specimen with electron-beam irradiation. As a result, the visualization of the real structure in the microscope image becomes increasingly difficult.

One recommended solution is to cool the specimen, that is, “Cryo” techniques. This “Cryo Note” introduces some of the diversified cryo-techniques. We sincerely hope your challenge to observe the “real structure” will be solved by “Cryo” methods.

This CryoNote includes:

Cryo History
A wide range of Cryo-techniques
Freezing
Sectioning / Fracturing
Etching (Ice sublimation)
Cryo-TEM
Freeze Substitution
Freeze Replication
Cryo-SEM
Low-Vacuum SEM and Cooling with Peltier element
Cryo-FIB
Cooling CP (Cryo-CP)

e-ABF (enhanced annular bright field image)

Thu, 10 Dec 2020 11:07:43 GMT

An e-ABF is observable as a "live image" with real-time signal processing of ABF and BF signals and it shows enhanced contrast of light atoms.