Electron Optic Documents

JEOL CRYO ARM 200 - BIBLIOGRAPHY

1. Young, Lucy C et al. “Destabilizing NF1 variants act in a dominant negative manner through neurofibromin dimerization.” Proceedings of the National Academy of Sciences of the United States of America vol. 120,5 (2023): e2208960120. doi:10.1073/pnas.2208960120
2. Pöll, Gisela et al. “Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors.” PloS one vol. 18,3 e0283698. 30 Mar. 2023, doi:10.1371/journal.pone.0283698
3. Katsyv, Alexander et al. “Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC.” Journal of the American Chemical Society vol. 145,10 (2023): 5696-5709. doi:10.1021/jacs.2c11683
4. Daiß, Julia L et al. “The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans.” Life science alliance vol. 5,11 e202201568. 1 Sep. 2022, doi:10.26508/lsa.202201568
5. 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
6. 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
7. 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
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
9. 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
10. 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
11. Oide, Mao et al. “Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo-electron microscopy.” The FEBS journal vol. 287,16 (2020): 3472-3493. doi:10.1111/febs.15224
12. Yamada, Yurika et al. “Cardiac muscle thin filament structures reveal calcium regulatory mechanism.” Nature communications vol. 11,1 153. 9 Jan. 2020, doi:10.1038/s41467-019-14008-1
13. Kato, Takayuki et al. “Structure of the native supercoiled flagellar hook as a universal joint.” Nature communications vol. 10,1 5295. 22 Nov. 2019, doi:10.1038/s41467-019-13252-9

JEOL CRYO ARM 300 - BIBLIOGRAPHY

1. Tanaka, Mayuki et al. “Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.” Nature chemical biology, 10.1038/s41589-023-01513-0. 24 Jan. 2024, doi:10.1038/s41589-023-01513-0
2. Tani, Kazutoshi et al. “High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum.” Communications biology vol. 7,1 176. 12 Feb. 2024, doi:10.1038/s42003-024-05863-w
3. Tomono, Junta et al. “Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.” Journal of biochemistry, mvae002. 16 Jan. 2024, doi:10.1093/jb/mvae002
4. Bloch, Yehudi et al. “Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23.” Nature structural & molecular biology, 10.1038/s41594-023-01190-6. 29 Jan. 2024, doi:10.1038/s41594-023-01190-6
5. Acar, Delphine Diana et al. “Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted.” EBioMedicine vol. 100 (2024): 104960. doi:10.1016/j.ebiom.2023.104960
6. Li, Liushuai et al. “Neutralizing monoclonal antibodies against the Gc fusion loop region of Crimean-Congo hemorrhagic fever virus.” PLoS pathogens vol. 20,2 e1011948. 1 Feb. 2024, doi:10.1371/journal.ppat.1011948
7. Artigas, Pablo et al. “A Na pump with reduced stoichiometry is up-regulated by brine shrimp in extreme salinities.” Proceedings of the National Academy of Sciences of the United States of America vol. 120,52 (2023): e2313999120. doi:10.1073/pnas.2313999120
8. Suzuki Yohei et al. “Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry.” ACS Catalysis 2023 13 (20), 13828-13837, doi: 10.1021/acscatal.3c03769
9. Akiba, Hiroki et al. “Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection.” Communications biology vol. 6,1 987. 27 Sep. 2023, doi:10.1038/s42003-023-05326-8
10. Liu, Qianyun et al. “Broadly neutralizing antibodies derived from the earliest COVID-19 convalescents protect mice from SARS-CoV-2 variants challenge.” Signal transduction and targeted therapy vol. 8,1 347. 14 Sep. 2023, doi:10.1038/s41392-023-01615-0
11. Bui, Han Ba et al. “Cryo-EM structures of human zinc transporter ZnT7 reveal the mechanism of Zn2+ uptake into the Golgi apparatus.” Nature communications vol. 14,1 4770. 8 Aug. 2023, doi:10.1038/s41467-023-40521-5
12. Yang, Shangyu et al. “Structural and functional insights into the modulation of T cell costimulation by monkeypox virus protein M2.” Nature communications vol. 14,1 5186. 25 Aug. 2023, doi:10.1038/s41467-023-40748-2
13. Abe, Kazuhiro et al. “Deep learning driven de novo drug design based on gastric proton pump structures.” Communications biology vol. 6,1 956. 19 Sep. 2023, doi:10.1038/s42003-023-05334-8
14. Zhao, Yan et al. “Cryo-EM structures of African swine fever virus topoisomerase.” mBio vol. 14,5 (2023): e0122823. doi:10.1128/mbio.01228-23
15. Torino, Stefania et al. “Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting.” Nature methods vol. 20,9 (2023): 1400-1408. doi:10.1038/s41592-023-01967-z
16. Anzai, Itsuki et al. “Characterization of a neutralizing antibody that recognizes a loop region adjacent to the receptor-binding interface of the SARS-CoV-2 spike receptor-binding domain.” Microbiology spectrum, e0365523. 28 Feb. 2024, doi:10.1128/spectrum.03655-23
17. Adachi Taiki et al. “Experimental and Theoretical Insights into Bienzymatic Cascade for Mediatorless Bioelectrochemical Ethanol Oxidation with Alcohol and Aldehyde Dehydrogenases.” ACS Catalysis 2023 13 (12), 7955-7965. doi: 10.1021/acscatal.3c01962
18. Li, Long et al. “Spatiotemporal Landscape for the Sophisticated Transformation of Protein Assemblies Defined by Multiple Supramolecular Interactions.” ACS nano vol. 17,15 (2023): 15001-15011. doi:10.1021/acsnano.3c04029
19. Fujita, Junso et al. “Structures of a FtsZ single protofilament and a double-helical tube in complex with a monobody.” Nature communications vol. 14,1 4073. 10 Jul. 2023, doi:10.1038/s41467-023-39807-5
20. Wang, Xiaoshen et al. “Structural insights into mechanisms of Argonaute protein-associated NADase activation in bacterial immunity.” Cell research vol. 33,9 (2023): 699-711. doi:10.1038/s41422-023-00839-7
21. De Gieter, Steven et al. “Sterol derivative binding to the orthosteric site causes conformational changes in an invertebrate Cys-loop receptor.” eLife vol. 12 e86029. 3 Jul. 2023, doi:10.7554/eLife.86029
22. Burton-Smith, Raymond N et al. “Six states of Enterococcus hirae V-type ATPase reveals non-uniform rotor rotation during turnover.” Communications biology vol. 6,1 755. 28 Jul. 2023, doi:10.1038/s42003-023-05110-8
23. Maki-Yonekura, Saori et al. “Measurement of charges and chemical bonding in a cryo-EM structure.” Communications chemistry vol. 6,1 98. 31 May. 2023, doi:10.1038/s42004-023-00900-x
24. Sleutel, Mike et al. “Structural analysis and architectural principles of the bacterial amyloid curli.” Nature communications vol. 14,1 2822. 17 May. 2023, doi:10.1038/s41467-023-38204-2
25. Isaacs, Ariel et al. “Structure and antigenicity of divergent Henipavirus fusion glycoproteins.” Nature communications vol. 14,1 3577. 16 Jun. 2023, doi:10.1038/s41467-023-39278-8
26. Gupta, Jyoti et al. “Plakophilin-3 Binds the Membrane and Filamentous Actin without Bundling F-Actin.” International journal of molecular sciences vol. 24,11 9458. 29 May. 2023, doi:10.3390/ijms24119458
27. Pei, Xudong et al. “Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer.” Nature communications vol. 14,1 3027. 25 May. 2023, doi:10.1038/s41467-023-38268-0
28. Ishimaru, Hanako et al. “Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.” Journal of virology, e0028623. 16 May. 2023, doi:10.1128/jvi.00286-23
29. Fernandez, Maricruz et al. “AFM-based force spectroscopy unravels stepwise formation of the DNA transposition complex in the widespread Tn3 family mobile genetic elements.” Nucleic acids research vol. 51,10 (2023): 4929-4941. doi:10.1093/nar/gkad241
30. Tsirigotaki, Alexandra et al. “Mechanism of receptor assembly via the pleiotropic adipokine Leptin.” Nature structural & molecular biology vol. 30,4 (2023): 551-563. doi:10.1038/s41594-023-00941-9
31. Kozai, Daisuke et al. “Recognition Mechanism of a Novel Gabapentinoid Drug, Mirogabalin, for Recombinant Human α2δ1, a Voltage-Gated Calcium Channel Subunit.” Journal of molecular biology vol. 435,10 (2023): 168049. doi:10.1016/j.jmb.2023.168049
32. Chen, Zhenghao et al. “Cryo-EM structures of human SPCA1a reveal the mechanism of Ca2+/Mn2+ transport into the Golgi apparatus.” Science advances vol. 9,9 (2023): eadd9742. doi:10.1126/sciadv.add9742
33. Himiyama, Tomoki et al. “Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins.” Bioconjugate chemistry, 10.1021/acs.bioconjchem.3c00057. 8 Mar. 2023, doi:10.1021/acs.bioconjchem.3c00057
34. Rangarajan, Erumbi S et al. “Distinct inter-domain interactions of dimeric versus monomeric α-catenin link cell junctions to filaments.” Communications biology vol. 6,1 276. 16 Mar. 2023, doi:10.1038/s42003-023-04610-x
35. Nagao, Ryo et al. “Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120.” Nature communications vol. 14,1 920. 17 Feb. 2023, doi:10.1038/s41467-023-36504-1
36. Fujita, Junso et al. “Epoxidized graphene grid for highly efficient high-resolution cryoEM structural analysis.” Scientific reports vol. 13,1 2279. 8 Feb. 2023, doi:10.1038/s41598-023-29396-0
37. Nakanishi, Atsuko et al. “Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding.” The Journal of biological chemistry, 102884. 7 Jan. 2023, doi:10.1016/j.jbc.2023.102884
38. Yin, Jiayi et al. “Structural transitions during the cooperative assembly of baculovirus single-stranded DNA-binding protein on ssDNA.” Nucleic acids research vol. 50,22 (2022): 13100-13113. doi:10.1093/nar/gkac1142
39. Wang, Xiaoshen et al. “Target RNA-guided protease activity in type III-E CRISPR-Cas system.” Nucleic acids research vol. 50,22 (2022): 12913-12923. doi:10.1093/nar/gkac1151
40. Rangarajan, Erumbi S et al. “The nematode HMP1/α-catenin has an extended α-helix when bound to actin filaments.” The Journal of biological chemistry, 102817. 17 Dec. 2022, doi:10.1016/j.jbc.2022.102817
41. Nakano, Atsuki et al. “Structural basis of unisite catalysis of bacterial F0F1-ATPase.” PNAS nexus vol. 1,3 pgac116. 11 Jul. 2022, doi:10.1093/pnasnexus/pgac116
42. Otsubo, Ryota et al. “Human antibody recognition and neutralization mode on the NTD and RBD domains of SARS-CoV-2 spike protein.” Scientific reports vol. 12,1 20120. 22 Nov. 2022, doi:10.1038/s41598-022-24730-4
43. Lemonidis, Kimon et al. “Structural and biochemical basis of interdependent FANCI-FANCD2 ubiquitination.” The EMBO journal, e111898. 17 Nov. 2022, doi:10.15252/embj.2022111898
44. Yu, Guimei et al. “Structure and function of a bacterial type III-E CRISPR-Cas7-11 complex.” Nature microbiology vol. 7,12 (2022): 2078-2088. doi:10.1038/s41564-022-01256-z
45. Shkumatov, Alexander V et al. “Structural insight into Tn3 family transposition mechanism.” Nature communications vol. 13,1 6155. 18 Oct. 2022, doi:10.1038/s41467-022-33871-z
46. Haney, Joanne et al. “Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles.” Nature microbiology vol. 7,11 (2022): 1879-1890. doi:10.1038/s41564-022-01242-5
47. Fréchin, Léo et al. “High-resolution cryo-EM performance comparison of two latest-generation cryo electron microscopes on the human ribosome.” Journal of structural biology, vol. 215,1 107905. 12 Oct. 2022, doi:10.1016/j.jsb.2022.107905
48. Li, Jiannan et al. “Structure of cyanobacterial photosystem I complexed with ferredoxin at 1.97 Å resolution.” Communications biology vol. 5,1 951. 12 Sep. 2022, doi:10.1038/s42003-022-03926-4
49. Manik, Mohammad K et al. “Cyclic ADP ribose isomers: Production, chemical structures, and immune signaling.” Science (New York, N.Y.) vol. 377,6614 (2022): eadc8969. doi:10.1126/science.adc8969
50. Maeda, Ryota et al. “A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron.” Communications biology vol. 5,1 669. 6 Jul. 2022, doi:10.1038/s42003-022-03630-3
51. Kawakami, Keisuke et al. “Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.” Nature communications vol. 13,1 3389. 17 Jun. 2022, doi:10.1038/s41467-022-30962-9
52. Yoshikawa, Tatsushi et al. “Multiple electron transfer pathways of tungsten-containing formate dehydrogenase in direct electron transfer-type bioelectrocatalysis.” Chemical communications (Cambridge, England) vol. 58,45 6478-6481. 1 Jun. 2022, doi:10.1039/d2cc01541b
53. 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
54. 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
55. 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
56. 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
57. 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
58. 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
59. 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
60. 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
61. 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
62. 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
63. 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
64. 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
65. 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
66. 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
67. 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
68. 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
69. 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
70. 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
71. 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
72. 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
73. 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
74. 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
75. Naitow, Hisashi et al. “Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release.” Communications biology vol. 3,1 488. 4 Sep. 2020, doi:10.1038/s42003-020-01217-4
76. 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
77. 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
78. Rennie, Martin L et al. “Differential functions of FANCI and FANCD2 ubiquitination stabilize ID2 complex on DNA.” EMBO reports vol. 21,7 (2020): e50133. doi:10.15252/embr.202050133
79. Yonekura, Koji et al. “A new cryo-EM system for electron 3D crystallography by eEFD.” Journal of structural biology vol. 206,2 (2019): 243-253. doi:10.1016/j.jsb.2019.03.009
80. Kato, Takayuki, et al. “CryoTEM with a Cold Field Emission Gun That Moves Structural Biology into a New Stage.” Microscopy and Microanalysis, vol. 25, no. S2, 2019, pp. 998–999., doi:10.1017/S1431927619005725.
81. Bhella, David. “Cryo-electron microscopy: an introduction to the technique, and considerations when working to establish a national facility.” Biophysical reviews vol. 11,4 (2019): 515-519. doi:10.1007/s12551-019-00571-w
82. Hamaguchi, Tasuku et al. “A new cryo-EM system for single particle analysis.” Journal of structural biology vol. 207,1 (2019): 40-48. doi:10.1016/j.jsb.2019.04.011