6YM0

Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab (crystal form 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.36 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.323 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth E]213Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
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
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
heavy chainB [auth H]228Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
light chainC [auth L]220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.36 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.323 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.474α = 90
b = 150.474β = 90
c = 241.579γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing
Vagabondphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2020-10-28
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary