7ND9

EM structure of SARS-CoV-2 Spike glycoprotein (one RBD up) in complex with COVOX-253H55L Fab

Summary for 7ND9

• Entry DOI: 10.2210/pdb7nd9/pdb
• Related: 7BEH 7BEI 7BEJ 7BEK 7BEL 7BEM 7BEN 7BEO 7BEP 7ND3 7ND8
• EMDB information: 12280
• Descriptor: Spike glycoprotein, COVOX-253H55L Fab heavy chain, COVOX-253H55L Fab light chain, ... (6 entities in total)
• Functional Keywords: sars-cov-2, antibody, germline, v-gene, receptor-binding-domain, spike, neutralisation, protection, glycosylation, valency, viral protein, immune system
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV); More
• Total number of polymer chains: 5
• Total formula weight: 488445.74

Authors

Duyvesteyn, H.M.E.,Zhao, Y.,Ren, J.,Stuart, D. (deposition date: 2021-01-30, release date: 2021-03-03, Last modification date: 2024-10-16)

Primary citation

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.
The antigenic anatomy of SARS-CoV-2 receptor binding domain.
Cell, 184:2183-, 2021

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 < 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.

PubMed: 33756110
DOI: 10.1016/j.cell.2021.02.032

Experimental method

ELECTRON MICROSCOPY (2.8 Å)