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Structure paper

TitleMapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.
Journal, issue, pagesCell, Vol. 183, Issue 4, Page 1024-1042.e21, Year 2020
Publish dateNov 12, 2020
AuthorsLuca Piccoli / Young-Jun Park / M Alejandra Tortorici / Nadine Czudnochowski / Alexandra C Walls / Martina Beltramello / Chiara Silacci-Fregni / Dora Pinto / Laura E Rosen / John E Bowen / Oliver J Acton / Stefano Jaconi / Barbara Guarino / Andrea Minola / Fabrizia Zatta / Nicole Sprugasci / Jessica Bassi / Alessia Peter / Anna De Marco / Jay C Nix / Federico Mele / Sandra Jovic / Blanca Fernandez Rodriguez / Sneha V Gupta / Feng Jin / Giovanni Piumatti / Giorgia Lo Presti / Alessandra Franzetti Pellanda / Maira Biggiogero / Maciej Tarkowski / Matteo S Pizzuto / Elisabetta Cameroni / Colin Havenar-Daughton / Megan Smithey / David Hong / Valentino Lepori / Emiliano Albanese / Alessandro Ceschi / Enos Bernasconi / Luigia Elzi / Paolo Ferrari / Christian Garzoni / Agostino Riva / Gyorgy Snell / Federica Sallusto / Katja Fink / Herbert W Virgin / Antonio Lanzavecchia / Davide Corti / David Veesler /
PubMed AbstractAnalysis 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. ...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.
External linksCell / PubMed:32991844 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.043 - 8.5 Å
Structure data

22491

7jv2

EMDB-22491, PDB-7jv2:
SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody Fab fragment (local refinement of the receptor-binding motif and Fab variable domains)
Method: EM (single particle) / Resolution: 3.5 Å

22492

7jv4

EMDB-22492, PDB-7jv4:
SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody (one RBD open)
Method: EM (single particle) / Resolution: 3.4 Å

22494

7jv6

EMDB-22494, PDB-7jv6:
SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody (closed conformation)
Method: EM (single particle) / Resolution: 3.0 Å

22497

7jva

EMDB-22497, PDB-7jva:
SARS-CoV-2 spike in complex with the S2A4 neutralizing antibody Fab fragment (local refinement of the receptor-binding domain and Fab variable domains)
Method: EM (single particle) / Resolution: 3.6 Å

22506

7jvc

EMDB-22506, PDB-7jvc:
SARS-CoV-2 spike in complex with the S2A4 neutralizing antibody Fab fragment
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-22507:
SARS-CoV-2 spike in complex with the S2H14 neutralizing antibody Fab fragment (two receptor-binding domains open)
Method: EM (single particle) / Resolution: 7.8 Å

EMDB-22508:
SARS-CoV-2 spike in complex with the S2H14 neutralizing antibody Fab fragment (three receptor-binding domains open)
Method: EM (single particle) / Resolution: 8.5 Å

22512

7jw0

EMDB-22512, PDB-7jw0:
SARS-CoV-2 spike in complex with the S304 neutralizing antibody Fab fragment
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-22516:
SARS-CoV-2 spike in complex with the S2X35 neutralizing antibody Fab fragment
Method: EM (single particle) / Resolution: 5.0 Å

EMDB-22517:
SARS-CoV-2 spike in complex with the S2X35 neutralizing antibody Fab fragment (local refinement of the receptor-binding motif and Fab variable domains)
Method: EM (single particle) / Resolution: 5.0 Å

PDB-7jx3:
Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

PDB-7jxc:
Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
Method: X-RAY DIFFRACTION / Resolution: 2.47 Å

PDB-7jxd:
Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-7jxe:
Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
Method: X-RAY DIFFRACTION / Resolution: 2.043 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-HOH:
WATER / Water

ChemComp-2PE:
NONAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / COVID-19 / spike glycoprotein / fusion protein / neutralizing antibodies / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN-IMMUNE SYSTEM complex / neutralizing monoclonal antibody / IMMUNE SYSTEM / neutralizing antibody / sarbecovirus

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