7BEP

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 Fabs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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:  
    7BEH, 7BEI, 7BEL, 7BEM, 7BEJ, 7BEK, 7BEP, 7BEN, 7BEO, 7NDC, 7NDD, 7NDA, 7NDB, 7ND7, 7ND8, 7ND5, 7ND6, 7ND9, 7ND3, 7ND4

  • 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
UniProt
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-384 heavy chainB [auth A], G [auth D]243Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COVOX-384 light chainC [auth B], H [auth F]227Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
S309 heavy chainI [auth G], D [auth H]232Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
S309 light chainJ [auth I], E [auth L]214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-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]6N/AN-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
PA [auth I], Z [auth L]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
R [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
GA [auth D], P [auth A]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
PEG
Query on PEG

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

Download Ideal Coordinates CCD File 
IA [auth F], KA [auth G], LA [auth G], U [auth H]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GLY
Query on GLY

Download Ideal Coordinates CCD File 
AA [auth L], JA [auth F], MA [auth G], OA [auth G], Q [auth A], W [auth H]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
BA [auth C], M [auth E], NA [auth G], V [auth H], X [auth H]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth C] , DA [auth D] , EA [auth D] , HA [auth F] , N [auth A] , O [auth A] , QA [auth I] , S [auth B] , 
CA [auth C],  DA [auth D],  EA [auth D],  HA [auth F],  N [auth A],  O [auth A],  QA [auth I],  S [auth B],  T [auth B],  Y [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.76α = 90
b = 113.221β = 90
c = 302.773γ = 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