7JVC

SARS-CoV-2 spike in complex with the S2A4 neutralizing antibody Fab fragment

Summary for 7JVC

• Entry DOI: 10.2210/pdb7jvc/pdb
• EMDB information: 22491 22492 22494 22497 22506 22507 22508
• Descriptor: Spike glycoprotein, S2A4 Fab heavy chain, S2A4 Fab light chain, ... (6 entities in total)
• Functional Keywords: sars-cov-2, covid-19, spike glycoprotein, fusion protein, neutralizing antibodies, viral protein-immune system complex, structural genomics, seattle structural genomics center for infectious disease, ssgcid, viral protein/immune system
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV); More
• Total number of polymer chains: 9
• Total formula weight: 581823.37

Authors

Park, Y.J.,Tortorici, M.A.,Walls, A.C.,Czudnochowski, N.,Seattle Structural Genomics Center for Infectious Disease (SSGCID),Snell, G.,Veesler, D. (deposition date: 2020-08-20, release date: 2020-10-14, Last modification date: 2024-10-23)

Primary citation

Piccoli, L.,Park, Y.J.,Tortorici, M.A.,Czudnochowski, N.,Walls, A.C.,Beltramello, M.,Silacci-Fregni, C.,Pinto, D.,Rosen, L.E.,Bowen, J.E.,Acton, O.J.,Jaconi, S.,Guarino, B.,Minola, A.,Zatta, F.,Sprugasci, N.,Bassi, J.,Peter, A.,De Marco, A.,Nix, J.C.,Mele, F.,Jovic, S.,Rodriguez, B.F.,Gupta, S.V.,Jin, F.,Piumatti, G.,Lo Presti, G.,Pellanda, A.F.,Biggiogero, M.,Tarkowski, M.,Pizzuto, M.S.,Cameroni, E.,Havenar-Daughton, C.,Smithey, M.,Hong, D.,Lepori, V.,Albanese, E.,Ceschi, A.,Bernasconi, E.,Elzi, L.,Ferrari, P.,Garzoni, C.,Riva, A.,Snell, G.,Sallusto, F.,Fink, K.,Virgin, H.W.,Lanzavecchia, A.,Corti, D.,Veesler, D.
Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.
Cell, 183:1024-1042.e21, 2020

PubMed Abstract: Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.

PubMed: 32991844
DOI: 10.1016/j.cell.2020.09.037

Experimental method

ELECTRON MICROSCOPY (3.3 Å)