Structure of the prefusion SARS-CoV-2 spike glycoprotein

Experimental Data Snapshot

  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.

Huo, J.Zhao, Y.Ren, J.Zhou, D.Duyvesteyn, H.M.E.Ginn, H.M.Carrique, L.Malinauskas, T.Ruza, R.R.Shah, P.N.M.Tan, T.K.Rijal, P.Coombes, N.Bewley, K.R.Tree, J.A.Radecke, J.Paterson, N.G.Supasa, P.Mongkolsapaya, J.Screaton, G.R.Carroll, M.Townsend, A.Fry, E.E.Owens, R.J.Stuart, D.I.

(2020) Cell Host Microbe 28: 445-454.e6

  • DOI: https://doi.org/10.1016/j.chom.2020.06.010
  • Primary Citation of Related Structures:  
    6YLA, 6YM0, 6YOR, 6Z97

  • PubMed Abstract: 

    There are as yet no licensed therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2, initiating conformational changes that drive membrane fusion. We find that the monoclonal antibody CR3022 binds the RBD tightly, neutralizing SARS-CoV-2, and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilizing CR3022 epitope is inaccessible in the prefusion spike, suggesting that CR3022 binding facilitates conversion to the fusion-incompetent post-fusion state. Cryogenic electron microscopy (cryo-EM) analysis confirms that incubation of spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope could be useful therapeutically, possibly in synergy with an antibody that blocks receptor attachment.

  • Organizational Affiliation

    Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK; The Rosalind Franklin Institute, Harwell Campus, OX11 0FA, UK; Protein Production UK, Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, OX11 0FA, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein,Fibritin
A, B, C
1,288Severe acute respiratory syndrome coronavirus 2Tequatrovirus T4
This entity is chimeric
Mutation(s): 5 
Gene Names: S2wac
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Find proteins for P10104 (Enterobacteria phage T4)
Explore P10104 
Go to UniProtKB:  P10104
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0DTC2P10104
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
D, E, F, G, H
D, E, F, G, H, I, J, K, L, M, N
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 3.40 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
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1
Wellcome TrustUnited Kingdom101122/Z/13/Z
CAMS Innovation Fund for Medical Sciences (CIFMS)China2018-I2M-2-002

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-09-23
    Changes: Database references, Structure summary