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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1016/j.cell.2021.02.032
  • Primary Citation of Related Structures:  
    7NDC, 7NDD, 7NDA, 7NDB, 7ND7, 7ND8, 7ND5, 7ND6, 7ND9, 7ND3

  • 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) ...

    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; Oxford University Hospitals NHS Foundation Trust, Oxford, UK. Electronic address: gavin.screaton@medsci.ox.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinF [auth C], A [auth E]205Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COVOX-253 heavy chainG [auth D], B [auth H]228Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COVOX-253 light chainH [auth F], C [auth L]215Homo sapiensMutation(s): 0 
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
COVOX-75 heavy chainD [auth A], I [auth G]232Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
COVOX-75 light chainE [auth B], J [auth I]214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChainsChain 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]3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 6 Unique
IDChainsName / 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
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
KA [auth G]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
DA [auth G], EA [auth G]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth F], N [auth E], O [auth E], U [auth B], W [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download Ideal Coordinates CCD File 
FA [auth G] , GA [auth G] , HA [auth G] , IA [auth G] , JA [auth G] , MA [auth I] , NA [auth I] , P [auth H] , 
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
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
CA [auth F], LA [auth I], M [auth E], V [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
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