Uncleavable Spike Protein of SARS-CoV-2 in Closed Conformation

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.1 of the entry. See complete history


SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects.

Wrobel, A.G.Benton, D.J.Xu, P.Roustan, C.Martin, S.R.Rosenthal, P.B.Skehel, J.J.Gamblin, S.J.

(2020) Nat Struct Mol Biol 27: 763-767

  • DOI: https://doi.org/10.1038/s41594-020-0468-7
  • Primary Citation of Related Structures:  
    6ZGE, 6ZGF, 6ZGG, 6ZGH, 6ZGI

  • PubMed Abstract: 

    SARS-CoV-2 is thought to have emerged from bats, possibly via a secondary host. Here, we investigate the relationship of spike (S) glycoprotein from SARS-CoV-2 with the S protein of a closely related bat virus, RaTG13. We determined cryo-EM structures for RaTG13 S and for both furin-cleaved and uncleaved SARS-CoV-2 S; we compared these with recently reported structures for uncleaved SARS-CoV-2 S. We also biochemically characterized their relative stabilities and affinities for the SARS-CoV-2 receptor ACE2. Although the overall structures of human and bat virus S proteins are similar, there are key differences in their properties, including a more stable precleavage form of human S and about 1,000-fold tighter binding of SARS-CoV-2 to human receptor. These observations suggest that cleavage at the furin-cleavage site decreases the overall stability of SARS-CoV-2 S and facilitates the adoption of the open conformation that is required for S to bind to the ACE2 receptor.

  • Organizational Affiliation

    Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK. antoni.wrobel@crick.ac.uk.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,287Severe acute respiratory syndrome coronavirus 2Mutation(s): 4 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
HA [auth A]
IA [auth A]
JA [auth A]
AB [auth C],
BB [auth C],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth B],
PA [auth B],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth B],
VA [auth C],
WA [auth C],
XA [auth C],
YA [auth C],
ZA [auth C]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomFC001078
The Francis Crick InstituteUnited KingdomFC001143

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-09-16
    Changes: Database references, Structure summary