7QNY

The receptor binding domain of SARS-CoV-2 spike glycoprotein in complex with COVOX-58 and COVOX-158 Fabs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.

Dejnirattisai, W.Huo, J.Zhou, D.Zahradnik, J.Supasa, P.Liu, C.Duyvesteyn, H.M.E.Ginn, H.M.Mentzer, A.J.Tuekprakhon, A.Nutalai, R.Wang, B.Dijokaite, A.Khan, S.Avinoam, O.Bahar, M.Skelly, D.Adele, S.Johnson, S.A.Amini, A.Ritter, T.G.Mason, C.Dold, C.Pan, D.Assadi, S.Bellass, A.Omo-Dare, N.Koeckerling, D.Flaxman, A.Jenkin, D.Aley, P.K.Voysey, M.Costa Clemens, S.A.Naveca, F.G.Nascimento, V.Nascimento, F.Fernandes da Costa, C.Resende, P.C.Pauvolid-Correa, A.Siqueira, M.M.Baillie, V.Serafin, N.Kwatra, G.Da Silva, K.Madhi, S.A.Nunes, M.C.Malik, T.Openshaw, P.J.M.Baillie, J.K.Semple, M.G.Townsend, A.R.Huang, K.A.Tan, T.K.Carroll, M.W.Klenerman, P.Barnes, E.Dunachie, S.J.Constantinides, B.Webster, H.Crook, D.Pollard, A.J.Lambe, T.Paterson, N.G.Williams, M.A.Hall, D.R.Fry, E.E.Mongkolsapaya, J.Ren, J.Schreiber, G.Stuart, D.I.Screaton, G.R.

(2022) Cell 185: 467-484.e15

  • DOI: https://doi.org/10.1016/j.cell.2021.12.046
  • Primary Citation of Related Structures:  
    7QNW, 7QNX, 7QNY

  • PubMed Abstract: 

    On 24 th November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.


  • Organizational Affiliation

    Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-58 heavy chain232Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-58 light chain214Homo 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
Surface glycoproteinC [auth E]202Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-158 heavy chainD [auth H]222Homo 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-158 light chainE [auth L]214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.762α = 90
b = 72.762β = 90
c = 416.202γ = 120
Software Package:
Software NamePurpose
GDAdata collection
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CAMS Innovation Fund for Medical Sciences (CIFMS)United Kingdom2018-I2M-2-002
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2022-10-26
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary