Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

[1]  Jared Adolf-Bryfogle,et al.  Automatically Fixing Errors in Glycoprotein Structures with Rosetta , 2018, Structure.

[2]  Erik Lindahl,et al.  New tools for automated high-resolution cryo-EM structure determination in RELION-3 , 2018, eLife.

[3]  Daniel Wrapp,et al.  Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis , 2018, Scientific Reports.

[4]  Jasenko Zivanov,et al.  A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis , 2018, bioRxiv.

[5]  David J. Harvey,et al.  Site-Specific Glycosylation of Virion-Derived HIV-1 Env Is Mimicked by a Soluble Trimeric Immunogen , 2018, Cell reports.

[6]  Xinquan Wang,et al.  Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2 , 2018, PLoS pathogens.

[7]  Thomas Strecker,et al.  Structure of the Lassa virus glycan shield provides a model for immunological resistance , 2018, Proceedings of the National Academy of Sciences.

[8]  M. Gray,et al.  An Antibody Targeting the Fusion Machinery Neutralizes Dual‐Tropic Infection and Defines a Site of Vulnerability on Epstein‐Barr Virus , 2018, Immunity.

[9]  Fang Li,et al.  Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins , 2018, PLoS pathogens.

[10]  A. McCoy,et al.  Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement , 2018, Acta crystallographica. Section D, Structural biology.

[11]  Conrad C. Huang,et al.  UCSF ChimeraX: Meeting modern challenges in visualization and analysis , 2018, Protein science : a publication of the Protein Society.

[12]  A. Walls,et al.  Glycan Shield and Fusion Activation of a Deltacoronavirus Spike Glycoprotein Fine-Tuned for Enteric Infections , 2017, Journal of Virology.

[13]  Ning Wang,et al.  Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus , 2017, PLoS pathogens.

[14]  Fang Li,et al.  Cryo-Electron Microscopy Structure of Porcine Deltacoronavirus Spike Protein in the Prefusion State , 2017, Journal of Virology.

[15]  A. Walls,et al.  Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion , 2017, Proceedings of the National Academy of Sciences.

[16]  Barney S. Graham,et al.  Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen , 2017, Proceedings of the National Academy of Sciences.

[17]  Yi Shi,et al.  Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains , 2017, Nature Communications.

[18]  D. Agard,et al.  MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy , 2017, Nature Methods.

[19]  David J. Fleet,et al.  cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination , 2017, Nature Methods.

[20]  Haixia Zhou,et al.  Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding , 2016, Cell Research.

[21]  G. Whittaker,et al.  Murine Leukemia Virus (MLV)-based Coronavirus Spike-pseudotyped Particle Production and Infection. , 2016, Bio-protocol.

[22]  S. Perlman,et al.  Introduction of neutralizing immunogenicity index to the rational design of MERS coronavirus subunit vaccines , 2016, Nature Communications.

[23]  S. Perlman,et al.  Proteolytic processing of Middle East respiratory syndrome coronavirus spikes expands virus tropism , 2016, Proceedings of the National Academy of Sciences.

[24]  Frank DiMaio,et al.  Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy , 2016, Nature Structural &Molecular Biology.

[25]  Bryan Briney,et al.  Holes in the Glycan Shield of the Native HIV Envelope Are a Target of Trimer-Elicited Neutralizing Antibodies. , 2016, Cell reports.

[26]  E. Lindahl,et al.  Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 , 2016, bioRxiv.

[27]  Young Do Kwon,et al.  Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B, and G , 2016, Cell.

[28]  Frank DiMaio,et al.  Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta , 2016, bioRxiv.

[29]  Lisa E. Gralinski,et al.  SARS-like WIV1-CoV poised for human emergence , 2016, Proceedings of the National Academy of Sciences.

[30]  Barney S. Graham,et al.  Pre-fusion structure of a human coronavirus spike protein , 2016, Nature.

[31]  F. Dimaio,et al.  Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer , 2016, Nature.

[32]  Lisa E. Gralinski,et al.  A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence , 2015, Nature Medicine.

[33]  Keith S Wilson,et al.  Privateer: software for the conformational validation of carbohydrate structures , 2015, Nature Structural &Molecular Biology.

[34]  A. McDowall,et al.  Broadly Neutralizing Antibody 8ANC195 Recognizes Closed and Open States of HIV-1 Env , 2015, Cell.

[35]  R. Baric,et al.  Prophylactic and postexposure efficacy of a potent human monoclonal antibody against MERS coronavirus , 2015, Proceedings of the National Academy of Sciences.

[36]  Kai Zhang,et al.  Gctf: Real-time CTF determination and correction , 2015, bioRxiv.

[37]  R. Baric,et al.  Two Mutations Were Critical for Bat-to-Human Transmission of Middle East Respiratory Syndrome Coronavirus , 2015, Journal of Virology.

[38]  Alan Brown,et al.  Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions , 2015, Acta crystallographica. Section D, Biological crystallography.

[39]  L. Pelkmans,et al.  Coronavirus Cell Entry Occurs through the Endo-/Lysosomal Pathway in a Proteolysis-Dependent Manner , 2014, PLoS pathogens.

[40]  G. Whittaker,et al.  Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein , 2014, Proceedings of the National Academy of Sciences.

[41]  Yan Li,et al.  Bat Origins of MERS-CoV Supported by Bat Coronavirus HKU4 Usage of Human Receptor CD26 , 2014, Cell Host & Microbe.

[42]  B. L. de Groot,et al.  A Designed Conformational Shift To Control Protein Binding Specificity** , 2014, Angewandte Chemie.

[43]  B. Korber,et al.  Characterization and Immunogenicity of a Novel Mosaic M HIV-1 gp140 Trimer , 2014, Journal of Virology.

[44]  Marion P G Koopmans,et al.  Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation , 2013, The Lancet Infectious Diseases.

[45]  R. Henderson,et al.  High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy☆ , 2013, Ultramicroscopy.

[46]  Amit Kapoor,et al.  Middle East Respiratory Syndrome Coronavirus in Bats, Saudi Arabia , 2013, Emerging infectious diseases.

[47]  J. Epstein,et al.  Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor , 2013, Nature.

[48]  Yi Shi,et al.  Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 , 2013, Nature.

[49]  Philip R. Evans,et al.  How good are my data and what is the resolution? , 2013, Acta crystallographica. Section D, Biological crystallography.

[50]  Christian Drosten,et al.  Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC , 2013, Nature.

[51]  Karl Mechtler,et al.  Unambiguous Phosphosite Localization using Electron-Transfer/Higher-Energy Collision Dissociation (EThcD) , 2013, Journal of proteome research.

[52]  Yong J. Kil,et al.  Byonic: Advanced Peptide and Protein Identification Software , 2012, Current protocols in bioinformatics.

[53]  Shaoxia Chen,et al.  Prevention of overfitting in cryo-EM structure determination , 2012, Nature Methods.

[54]  Brendan MacLean,et al.  Bioinformatics Applications Note Gene Expression Skyline: an Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments , 2022 .

[55]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[56]  Pauline M Rudd,et al.  Identification of N-linked carbohydrates from severe acute respiratory syndrome (SARS) spike glycoprotein , 2010, Virology.

[57]  W. Kabsch.  XDS , 2010, Acta crystallographica. Section D, Biological crystallography.

[58]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[59]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[60]  F. Taguchi,et al.  Two-Step Conformational Changes in a Coronavirus Envelope Glycoprotein Mediated by Receptor Binding and Proteolysis , 2009, Journal of Virology.

[61]  G. Sciara,et al.  Production and biophysical characterization of the CorA transporter from Methanosarcina mazei. , 2009, Analytical biochemistry.

[62]  M Radermacher,et al.  DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy. , 2009, Journal of structural biology.

[63]  G. Whittaker,et al.  Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites , 2009, Proceedings of the National Academy of Sciences.

[64]  Christopher Irving,et al.  Appion: an integrated, database-driven pipeline to facilitate EM image processing. , 2009, Journal of structural biology.

[65]  R. Baric,et al.  Structural Basis for Potent Cross-Neutralizing Human Monoclonal Antibody Protection against Lethal Human and Zoonotic Severe Acute Respiratory Syndrome Coronavirus Challenge , 2008, Journal of Virology.

[66]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[67]  Silke Stertz,et al.  The intracellular sites of early replication and budding of SARS-coronavirus , 2007, Virology.

[68]  Conrad C. Huang,et al.  Visualizing density maps with UCSF Chimera. , 2007, Journal of structural biology.

[69]  Kevin Cowtan,et al.  The Buccaneer software for automated model building , 2006 .

[70]  Kevin Cowtan,et al.  The Buccaneer software for automated model building. 1. Tracing protein chains. , 2006, Acta crystallographica. Section D, Biological crystallography.

[71]  Y. Guan,et al.  SARS-CoV Infection in a Restaurant from Palm Civet , 2005, Emerging infectious diseases.

[72]  Jonathan H. Epstein,et al.  Bats Are Natural Reservoirs of SARS-Like Coronaviruses , 2005, Science.

[73]  S. Harrison,et al.  Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed with Receptor , 2005, Science.

[74]  Anchi Cheng,et al.  Automated molecular microscopy: the new Leginon system. , 2005, Journal of structural biology.

[75]  Chengsheng Zhang,et al.  Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2 , 2005, The EMBO journal.

[76]  G. Bricogne,et al.  Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. , 2004, Acta crystallographica. Section D, Biological crystallography.

[77]  Fei Long,et al.  REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. , 2004, Acta crystallographica. Section D, Biological crystallography.

[78]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[79]  B. Murphy,et al.  An efficient method to make human monoclonal antibodies from memory B cells: potent neutralization of SARS coronavirus , 2004, Nature Medicine.

[80]  Xiaolei Yin,et al.  Identification of an Antigenic Determinant on the S2 Domain of the Severe Acute Respiratory Syndrome Coronavirus Spike Glycoprotein Capable of Inducing Neutralizing Antibodies , 2004, Journal of Virology.

[81]  M. Ng,et al.  Proliferative growth of SARS coronavirus in Vero E6 cells. , 2003, The Journal of general virology.

[82]  R. Henderson,et al.  Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. , 2003, Journal of molecular biology.

[83]  H. Perreault,et al.  Mass Spectrometric Characterization of Proteins from the SARS Virus , 2003, Molecular & Cellular Proteomics.

[84]  H. Vennema,et al.  The Viral Spike Protein Is Not Involved in the Polarized Sorting of Coronaviruses in Epithelial Cells , 1998, Journal of Virology.