7BEN

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253 and COVOX-75 Fabs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7BEJ


Literature

The antigenic anatomy of SARS-CoV-2 receptor binding domain.

Dejnirattisai, W.Zhou, D.Ginn, H.M.Duyvesteyn, H.M.E.Supasa, P.Case, J.B.Zhao, Y.Walter, T.S.Mentzer, A.J.Liu, C.Wang, B.Paesen, G.C.Slon-Campos, J.Lopez-Camacho, C.Kafai, N.M.Bailey, A.L.Chen, R.E.Ying, B.Thompson, C.Bolton, J.Fyfe, A.Gupta, S.Tan, T.K.Gilbert-Jaramillo, J.James, W.Knight, M.Carroll, M.W.Skelly, D.Dold, C.Peng, Y.Levin, R.Dong, T.Pollard, A.J.Knight, J.C.Klenerman, P.Temperton, N.Hall, D.R.Williams, M.A.Paterson, N.G.Bertram, F.K.R.Siebert, C.A.Clare, D.K.Howe, A.Radecke, J.Song, Y.Townsend, A.R.Huang, K.A.Fry, E.E.Mongkolsapaya, J.Diamond, M.S.Ren, J.Stuart, D.I.Screaton, G.R.

(2021) Cell 184: 2183

  • DOI: https://doi.org/10.1016/j.cell.2021.02.032
  • Primary Citation of Related Structures:  
    7BEH, 7BEI, 7BEJ, 7BEK, 7BEL, 7BEM, 7BEN, 7BEO, 7BEP, 7ND3, 7ND4, 7ND5, 7ND6, 7ND7, 7ND8, 7ND9, 7NDA, 7NDB, 7NDC, 7NDD

  • PubMed Abstract: 

    Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC 50  < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.


  • Organizational Affiliation

    Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth E],
F [auth C]
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-253 heavy chainB [auth H],
G [auth D]
228Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-253 light chainC [auth L],
H [auth F]
215Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-75 heavy chainD [auth A],
I [auth G]
232Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
COVOX-75 light chainE [auth B],
J [auth I]
214Homo sapiensMutation(s): 0 
Entity Groups  
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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
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG6
Query on PG6

Download Ideal Coordinates CCD File 
BA [auth F],
R [auth L]
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
IOD
Query on IOD

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KA [auth G]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
PEG
Query on PEG

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DA [auth G],
EA [auth G]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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AA [auth F],
N [auth E],
O [auth E],
U [auth B],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR
Query on BR

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FA [auth G]
GA [auth G]
HA [auth G]
IA [auth G]
JA [auth G]
FA [auth G],
GA [auth G],
HA [auth G],
IA [auth G],
JA [auth G],
MA [auth I],
NA [auth I],
P [auth H],
Q [auth H],
S [auth A],
T [auth A],
X [auth B],
Y [auth B],
Z [auth D]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
IMD
Query on IMD

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CA [auth F],
LA [auth I],
M [auth E],
V [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.188α = 90
b = 149.794β = 90
c = 229.099γ = 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: 2021-04-07
    Changes: Database references
  • Version 1.2: 2021-04-28
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-31
    Changes: Refinement description