[1] FULLER S D, BERRIMAN J A, BUTCHER S J, et al. Low pH induces swiveling of the glycoprotein heterodimers in the Semliki forest virus spike complex[J]. Cell, 1995, 81(5): 715-725.
[2] BOTTCHER B, WYNNE S A, CROWTHER R A. Letters to nature determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy[J]. 1997, 386(March): 0-3.
[3] YU X, GE P, JIANG J, et al. Atomic model of CPV reveals the mechanism used by this single-shelled virus to economically carry out functions conserved in multishelled reoviruses[J]. Structure, 2011, 19(5): 652-661.
[4] ZHANG X, GE P, YU X, et al. Cryo-EM structure of the mature dengue virus at 3.5-Å resolution[J]. Nature Structural and Molecular Biology, 2013, 20(1): 105-110.
[5] ZHANG X, SUN S, XIANG Y, et al. Structure of Sputnik, a virophage, at 3.5-Å resolution[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(45): 18431-18436.
[6] ZHANG X, SETTEMBRE E, XU C, et al. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction[J]. 2008, 105(6): 1867-1872.
[7] YU X, JIN L, ZHOU Z H. structure of cytoplasmic polyhedrosis virus by Cryo-electron microscopy[J]. 2008, 453(May): 415-420.
[8] SHAIKH T R, GAO H, BAXTER W T, et al. Spider image processing for single-particle reconstruction of biological macromolecules from electron micrographs[J]. Nature Protocols, 2008, 3(12): 1941-1974.
[9] LUDTKE S J, JAKANA J, SONG J L, et al. A 11.5 Å single particle reconstruction of GroEL using EMAN[J]. Journal of Molecular Biology, 2001, 314(2): 253-262.
[10] YAN X, SINKOVITS R S, BAKER T S. AUTO3DEM-an automated and high throughput program for image reconstruction of icosahedral particles[J]. Journal of Structural Biology, 2007, 157(1): 73-82.
[11] LIANG Y, KE E Y, ZHOU Z H. IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database[J]. Journal of Structural Biology, 2002, 137(3): 292-304.
[12] GRIGORIEFF N. FREALIGN: High-resolution refinement of single particle structures[J]. Journal of Structural Biology, 2007, 157(1): 117-125.
[13] SUN C, GONZALEZ B, VAGO F S, et al. High resolution single particle Cryo-EM refinement using JSPR[J].Progress in Biophysics and Molecular Biology, 2020.
[14] YANG C, JIANG W, CHEN D H, et al. Estimating contrast transfer function and associated parameters by constrained non-linear optimization[J]. Journal of Microscopy, 2009, 233(3): 391-403.
[15] YU G, LI K, LIU Y, et al. An algorithm for estimation and correction of anisotropic magnification distortion of Cryo-EM images without need of pre-calibration[J]. Journal of Structural Biology, 2016, 195(2): 207-215.
[16] LI X, MOONEY P, ZHENG S, et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle Cryo-EM[J]. Nature Methods, 2013, 10(6): 584-590.
[17] SCHERES S H W. RELION: implementation of a Bayesian approach to Cryo-EM structure determination[J]. Journal of Structural Biology, 2012, 180(3): 519-530.
[18] SUN S, KONDABAGIL K, DRAPER B, et al. The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces[J]. Cell, 2008, 135(7): 1251-1262.
[19] JIANG W, CHANG J, JAKANA J, et al. Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus[J]. Nature, 2006, 439(7076): 612-616.
[20] DAI X, LI Z, LAI M, et al. In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus[J]. Nature, 2017, 541(7635): 112-116.
[21] LIU H, CHENG L. Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus[J]. Science, 2015, 349(6254): 1347-1350.
[22] ZHU L, SUN Y, FAN J, et al. Structures of Coxsackievirus A10 unveil the molecular mechanisms of receptor binding and viral uncoating[J]. Nature Communications, 2018, 9(1).
[23] ZHANG Y, KOSTYUCHENKO V A, ROSSMANN M G. Structural analysis of viral nucleocapsids by subtraction of partial projections[J]. Journal of Structural Biology, 2007, 157(2): 356-364.
[24] HUISKONEN J T, JÄÄLINOJA H T, BRIGGS J A G, et al. Structure of a hexameric RNA packaging motor in a viral polymerase complex[J]. Journal of Structural Biology, 2007, 158(2): 156-164.
[25] DEROSIER D J. Correction of high-resolution data for curvature of the Ewald sphere[J]. Ultramicroscopy, 2000, 81(2): 83-98.
[26] WOLF M, DEROSIER D J, GRIGORIEFF N. Ewald sphere correction for single-particle electron microscopy[J]. Ultramicroscopy, 2006, 106(4/5): 376-382.
[27] LEONG P A, YU X, ZHOU Z H, et al. Correcting for the Ewald sphere in high-resolution single-particle reconstructions [M/OL] //Methods in Enzymology: Vol. 482. 1. Elsevier Inc., 2010.
[28] LEONG P A. Computational challenges in high-resolution Cryo-electron microscopy[J]. 2009.
[29] ZHU D, WANG X, FANG Q, et al. Pushing the resolution limit by correcting the Ewald reconstructions[J]. Nature Communications,2018: 1-7.
[30] YUAN S, WANG J, ZHU D, et al. Cryo-EM structure of a herpesvirus capsid at 3.1 Å[J]. Science, 2018, 360(6384): 1-30.
[31] FANG Q, ZHU D, AGARKOVA I, et al. Near-atomic structure of a giant virus[J]. Nature Communications,2019, 10(1).
[32] WANG N, ZHAO D, WANG J, et al. Architecture of African swine fever virus and implications for viral assembly[J]. Science, 2019, 366(6465): 640-644.
[33] LIU S, LUO Y, WANG Y, et al. Cryo-EM Structure of the African Swine Fever Virus[J]. Cell Host and Microbe, 2019, 26(6): 836-843.e3.
[34] CHEN L, WANG M, ZHU D, et al. Implication for alphavirus host-cell entry and assembly indicated by a 3.5Å resolution Cryo-EM structure[J]. Nature Communications, 2018, 9(1).
[35] WANG A, ZHOU F, LIU C, et al. Structure of infective Getah virus at 2.8 Å resolution determined by Cryo-electron microscopy[J]. Cell Discovery, 2022, 8(1).
[36] FANG Q, TANG W C, FOKINE A, et al. Structures of a large prolate virus capsid in unexpanded and expanded states generate insights into the icosahedral virus assembly[J]. Proceedings of the National Academy of Sciences of the United States of America, 2022, 119(40): 1-12.
[37] SHAO Q, AGARKOVA I V, NOEL E A, et al. Structure of giant virus Paramecium bursaria chlorella virus 1[J]. 2022.
[38] XIE Q, YOSHIOKA C K, CHAPMAN M S. Adeno-associated virus (AAV-DJ)—Cryo-EM structure at 1.56 Å resolution[J]. 2020: 1-15.
[39] RUSSO C J, HENDERSON R. Ewald sphere correction using a single side-band image processing algorithm[J]. Ultramicroscopy, 2018, 187: 26-33.
[40] ILCA S L, KOTECHA A, SUN X, et al. Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes[J]. Nature Communications, 2015, 6: 1-8.
[41] MATTEI S, TAN A, GLASS B, et al. High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation[J]. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(40): E9401-E9410.
[42] SCHUR F K M, OBR M, HAGEN W J H, et al. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation [J]. Science, 2016, 353(6298): 506-508.
[43] TUROŇOVÁ B, SCHUR F K M, WAN W, et al. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4 Å[J]. Journal of Structural Biology, 2017, 199(3): 187-195.
[44] TEGUNOV D, XUE L, DIENEMANN C, et al. Multi-particle Cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.7 Å inside cells[J]. 期刊名,2020,卷(期):起始页码-终止页码??.
[45] 张佳星,陈勇,李赛. 冷冻电镜断层成像技术破解重构新冠病毒全分子结构难题[J]. 电子显微学报, 2020, 39(6): 6-8.
[46] KE Z, OTON J, QU K, et al. Structures and distributions of SARS-CoV-2 spike proteins on intact virions[J]. Nature, 2020, 588(7838): 498-502.
[47] TUROŇOVÁ B, SIKORA M, SCHÜRMANN C, et al. In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges[J]. Science, 2020, 370(6513): 203-208.
[48] TAI L, ZHU G, YANG M, et al. Nanometer-resolution in situ structure of the SARS-CoV-2 postfusion spike protein[J]. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118(48): 1-8.
[49] YAO H, SONG Y, CHEN Y, et al. Molecular architecture of the SARS-CoV-2 virus[J]. Cell, 2020, 183(3): 730-738.e13.
[50] VOLLMER B, PRAŽÁK V, VASISHTAN D, et al. The prefusion structure of herpes simplex virus glycoprotein B[J]. 2020(Sep): 1-12.
[51] HIMES B A, ZHANG P. emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging[J]. Nature Methods, 2018, 15(11): 955-961.
[52] CHENG J, LI B, SI L, et al. Determining structures in a native environment using single-particle cryoelectron microscopy images[J]. The Innovation, 2021, 2(4): 100166.