7NEH

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera.

Supasa, P.Zhou, D.Dejnirattisai, W.Liu, C.Mentzer, A.J.Ginn, H.M.Zhao, Y.Duyvesteyn, H.M.E.Nutalai, R.Tuekprakhon, A.Wang, B.Paesen, G.C.Slon-Campos, J.Lopez-Camacho, C.Hallis, B.Coombes, N.Bewley, K.R.Charlton, S.Walter, T.S.Barnes, E.Dunachie, S.J.Skelly, D.Lumley, S.F.Baker, N.Shaik, I.Humphries, H.E.Godwin, K.Gent, N.Sienkiewicz, A.Dold, C.Levin, R.Dong, T.Pollard, A.J.Knight, J.C.Klenerman, P.Crook, D.Lambe, T.Clutterbuck, E.Bibi, S.Flaxman, A.Bittaye, M.Belij-Rammerstorfer, S.Gilbert, S.Hall, D.R.Williams, M.A.Paterson, N.G.James, W.Carroll, M.W.Fry, E.E.Mongkolsapaya, J.Ren, J.Stuart, D.I.Screaton, G.R.

(2021) Cell 184: 2201

  • DOI: https://doi.org/10.1016/j.cell.2021.02.033
  • Primary Citation of Related Structures:  
    7NEG, 7NEH

  • PubMed Abstract: 

    SARS-CoV-2 has caused over 2 million deaths in little over a year. Vaccines are being deployed at scale, aiming to generate responses against the virus spike. The scale of the pandemic and error-prone virus replication is leading to the appearance of mutant viruses and potentially escape from antibody responses. Variant B.1.1.7, now dominant in the UK, with increased transmission, harbors 9 amino acid changes in the spike, including N501Y in the ACE2 interacting surface. We examine the ability of B.1.1.7 to evade antibody responses elicited by natural SARS-CoV-2 infection or vaccination. We map the impact of N501Y by structure/function analysis of a large panel of well-characterized monoclonal antibodies. B.1.1.7 is harder to neutralize than parental virus, compromising neutralization by some members of a major class of public antibodies through light-chain contacts with residue 501. However, widespread escape from monoclonal antibodies or antibody responses generated by natural infection or vaccination was not observed.


  • 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-269 Fab heavy chainA [auth H]222Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-269 fab light chainB [auth L]215Homo 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
Spike glycoproteinC [auth E]205Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
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
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
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-glucopyranoseD [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
P [auth L]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
T [auth L]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
E [auth H]
F [auth H]
G [auth H]
AA [auth E],
BA [auth E],
E [auth H],
F [auth H],
G [auth H],
I [auth H],
J [auth H],
K [auth H],
L,
M [auth L],
N [auth L],
Q [auth L],
R [auth L],
S [auth L],
U [auth E],
V [auth E],
W [auth E],
X [auth E],
Z [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
H,
O [auth L],
Y [auth E]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth E]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.812α = 90
b = 149.712β = 90
c = 145.906γ = 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)China2018-I2M-2-002

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2021-04-28
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description