7OR9

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and COVOX-278 Fabs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.

Liu, C.Ginn, H.M.Dejnirattisai, W.Supasa, P.Wang, B.Tuekprakhon, A.Nutalai, R.Zhou, D.Mentzer, A.J.Zhao, Y.Duyvesteyn, H.M.E.Lopez-Camacho, C.Slon-Campos, J.Walter, T.S.Skelly, D.Johnson, S.A.Ritter, T.G.Mason, C.Costa Clemens, S.A.Gomes Naveca, F.Nascimento, V.Nascimento, F.Fernandes da Costa, C.Resende, P.C.Pauvolid-Correa, A.Siqueira, M.M.Dold, C.Temperton, N.Dong, T.Pollard, A.J.Knight, J.C.Crook, D.Lambe, T.Clutterbuck, E.Bibi, S.Flaxman, A.Bittaye, M.Belij-Rammerstorfer, S.Gilbert, S.C.Malik, T.Carroll, M.W.Klenerman, P.Barnes, E.Dunachie, S.J.Baillie, V.Serafin, N.Ditse, Z.Da Silva, K.Paterson, N.G.Williams, M.A.Hall, D.R.Madhi, S.Nunes, M.C.Goulder, P.Fry, E.E.Mongkolsapaya, J.Ren, J.Stuart, D.I.Screaton, G.R.

(2021) Cell 184: 4220-4236.e13

  • DOI: https://doi.org/10.1016/j.cell.2021.06.020
  • Primary Citation of Related Structures:  
    7OR9, 7ORA, 7ORB

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone progressive change, with variants conferring advantage rapidly becoming dominant lineages, e.g., B.1.617. With apparent increased transmissibility, variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the United Kingdom. Here we study the ability of monoclonal antibodies and convalescent and vaccine sera to neutralize B.1.617.1 and B.1.617.2, complement this with structural analyses of Fab/receptor binding domain (RBD) complexes, and map the antigenic space of current variants. Neutralization of both viruses is reduced compared with ancestral Wuhan-related strains, but there is no evidence of widespread antibody escape as seen with B.1.351. However, B.1.351 and P.1 sera showed markedly more reduction in neutralization of B.1.617.2, suggesting that individuals infected previously by these variants may be more susceptible to reinfection by B.1.617.2. This observation provides important new insights for immunization policy with future variant vaccines in non-immune populations.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1A [auth E]205Severe 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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-222 Fab heavy chainB [auth A]224Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-222 Fab light chainC [auth B]214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-278 Fab heavy chainD [auth H]228Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-278 Fab light chainE [auth L]215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

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-glucopyranoseF [auth C]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
M [auth H]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth E],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth E],
I [auth E],
J [auth A],
L [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.73α = 90
b = 114.47β = 90
c = 177.93γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
GDAdata collection
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)China2018-I2M-2-002

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references
  • Version 1.2: 2021-08-18
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary