7ND8

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-384 Fab

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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, 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) ...

    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 glycoproteinA, B, C1288Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
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UniProt GroupP0DTC2
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COVOX-384 Fab heavy chainD [auth H]243Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COVOX-384 Fab light chainE [auth L]227Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F [auth D],
G [auth E],
H [auth F],
I [auth G],
J [auth I],
F [auth D],
G [auth E],
H [auth F],
I [auth G],
J [auth I],
K [auth J],
L [auth K],
M,
N,
O,
P,
Q,
R,
S,
T
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth B],
EA [auth B],
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
NA [auth B],
OA [auth C],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

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