6ZWV

Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: 3 Closed RBDs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures and distributions of SARS-CoV-2 spike proteins on intact virions.

Ke, Z.Oton, J.Qu, K.Cortese, M.Zila, V.McKeane, L.Nakane, T.Zivanov, J.Neufeldt, C.J.Cerikan, B.Lu, J.M.Peukes, J.Xiong, X.Krausslich, H.G.Scheres, S.H.W.Bartenschlager, R.Briggs, J.A.G.

(2020) Nature 588: 498-502

  • DOI: 10.1038/s41586-020-2665-2
  • Primary Citation of Related Structures:  
    6ZWV

  • PubMed Abstract: 
  • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virions are surrounded by a lipid bilayer from which spike (S) protein trimers protrude 1 . Heavily glycosylated S trimers bind to the angiotensin-converting enzyme 2 receptor an ...

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virions are surrounded by a lipid bilayer from which spike (S) protein trimers protrude 1 . Heavily glycosylated S trimers bind to the angiotensin-converting enzyme 2 receptor and mediate entry of virions into target cells 2-6 . S exhibits extensive conformational flexibility: it modulates exposure of its receptor-binding site and subsequently undergoes complete structural rearrangement to drive fusion of viral and cellular membranes 2,7,8 . The structures and conformations of soluble, overexpressed, purified S proteins have been studied in detail using cryo-electron microscopy 2,7,9-12 , but the structure and distribution of S on the virion surface remain unknown. Here we applied cryo-electron microscopy and tomography to image intact SARS-CoV-2 virions and determine the high-resolution structure, conformational flexibility and distribution of S trimers in situ on the virion surface. These results reveal the conformations of S on the virion, and provide a basis from which to understand interactions between S and neutralizing antibodies during infection or vaccination.


    Organizational Affiliation

    Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK. jbriggs@mrc-lmb.cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinABC1273Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
4, 6, 9, BA, F, Q, S, V, X, b, k, m, p, r, v
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, B, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-CoG-648432
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/16
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_A025_1013
German Research Foundation (DFG)Germany240245660-SFB 1129
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History 

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references
  • Version 1.2: 2020-09-02
    Changes: Database references
  • Version 1.3: 2020-12-30
    Changes: Database references