7PRY

Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with COVOX-45 and beta-6 Fabs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.

Liu, C.Zhou, D.Nutalai, R.Duyvesteyn, H.M.E.Tuekprakhon, A.Ginn, H.M.Dejnirattisai, W.Supasa, P.Mentzer, A.J.Wang, B.Case, J.B.Zhao, Y.Skelly, D.T.Chen, R.E.Johnson, S.A.Ritter, T.G.Mason, C.Malik, T.Temperton, N.Paterson, N.G.Williams, M.A.Hall, D.R.Clare, D.K.Howe, A.Goulder, P.J.R.Fry, E.E.Diamond, M.S.Mongkolsapaya, J.Ren, J.Stuart, D.I.Screaton, G.R.

(2022) Cell Host Microbe 30: 53

  • DOI: https://doi.org/10.1016/j.chom.2021.11.013
  • Primary Citation of Related Structures:  
    7PRY, 7PRZ, 7PS0, 7PS1, 7PS2, 7PS3, 7PS4, 7PS5, 7PS6, 7PS7, 7Q0G, 7Q0H, 7Q0I, 7Q6E, 7Q9F, 7Q9G, 7Q9I, 7Q9J, 7Q9K, 7Q9M, 7Q9P

  • PubMed Abstract: 

    Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta-infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor-binding domain (RBD). Two of these RBD-binding mAbs recognize a neutralizing epitope conserved between SARS-CoV-1 and -2, while 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y, including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses.


  • Organizational Affiliation

    Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-45 Fab heavy chain
A, F
226Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-45 Fab light chain
B, G
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-6 Fab heavy chainC [auth H],
H [auth C]
228Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-6 Fab light chainD [auth L],
I [auth D]
215Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1E,
J [auth I]
210Severe acute respiratory syndrome coronavirus 2Mutation(s): 3 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
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Go to UniProtKB:  P0DTC2
Entity Groups  
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UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J],
L [auth K]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.393α = 90
b = 166.778β = 108.518
c = 120.18γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

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
CAMS Innovation Fund for Medical Sciences (CIFMS)United Kingdom2018-I2M-2-002

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2021-12-22
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2021-12-29
    Changes: Database references
  • Version 1.3: 2022-01-26
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description