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Yorodumi- PDB-6zdh: SARS-CoV-2 Spike glycoprotein in complex with a neutralizing anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zdh | ||||||||||||
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Title | SARS-CoV-2 Spike glycoprotein in complex with a neutralizing antibody EY6A Fab | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / EY6a / RBD / Spike glycoprotein / SARS-CoV-2 / human neutralizing antibody / immune system | ||||||||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Duyvesteyn, H.M.E. / Zhou, D. / Zhao, Y. / Fry, E.E. / Ren, J. / Stuart, D.I. | ||||||||||||
Funding support | United Kingdom, China, 3items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient. Authors: Daming Zhou / Helen M E Duyvesteyn / Cheng-Pin Chen / Chung-Guei Huang / Ting-Hua Chen / Shin-Ru Shih / Yi-Chun Lin / Chien-Yu Cheng / Shu-Hsing Cheng / Yhu-Chering Huang / Tzou-Yien Lin / ...Authors: Daming Zhou / Helen M E Duyvesteyn / Cheng-Pin Chen / Chung-Guei Huang / Ting-Hua Chen / Shin-Ru Shih / Yi-Chun Lin / Chien-Yu Cheng / Shu-Hsing Cheng / Yhu-Chering Huang / Tzou-Yien Lin / Che Ma / Jiandong Huo / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila Rijal / Robert F Donat / Kerry Godwin / Karen R Buttigieg / Julia A Tree / Julika Radecke / Neil G Paterson / Piyada Supasa / Juthathip Mongkolsapaya / Gavin R Screaton / Miles W Carroll / Javier Gilbert-Jaramillo / Michael L Knight / William James / Raymond J Owens / James H Naismith / Alain R Townsend / Elizabeth E Fry / Yuguang Zhao / Jingshan Ren / David I Stuart / Kuan-Ying A Huang / Abstract: The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID- ...The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID-19 and have shown that it neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds the receptor binding domain (RBD) of the viral spike glycoprotein tightly (K of 2 nM), and a 2.6-Å-resolution crystal structure of an RBD-EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues within this footprint are key to stabilizing the pre-fusion spike. Cryo-EM analyses of the pre-fusion spike incubated with EY6A Fab reveal a complex of the intact spike trimer with three Fabs bound and two further multimeric forms comprising the destabilized spike attached to Fab. EY6A binds what is probably a major neutralizing epitope, making it a candidate therapeutic for COVID-19. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zdh.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zdh.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6zdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zdh_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6zdh_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6zdh_validation.xml.gz | 108.2 KB | Display | |
Data in CIF | 6zdh_validation.cif.gz | 166 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/6zdh ftp://data.pdbj.org/pub/pdb/validation_reports/zd/6zdh | HTTPS FTP |
-Related structure data
Related structure data | 11174MC 6zczC 6zdgC 6zerC 6zfoC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 142399.375 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | Mass: 24346.273 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Antibody | Mass: 23315.855 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 42.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.1_3865: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144680 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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