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Structure paper

TitleN-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2.
Journal, issue, pagesCell, Vol. 184, Issue 9, Page 2332-2347.e16, Year 2021
Publish dateApr 29, 2021
AuthorsMatthew McCallum / Anna De Marco / Florian A Lempp / M Alejandra Tortorici / Dora Pinto / Alexandra C Walls / Martina Beltramello / Alex Chen / Zhuoming Liu / Fabrizia Zatta / Samantha Zepeda / Julia di Iulio / John E Bowen / Martin Montiel-Ruiz / Jiayi Zhou / Laura E Rosen / Siro Bianchi / Barbara Guarino / Chiara Silacci Fregni / Rana Abdelnabi / Shi-Yan Caroline Foo / Paul W Rothlauf / Louis-Marie Bloyet / Fabio Benigni / Elisabetta Cameroni / Johan Neyts / Agostino Riva / Gyorgy Snell / Amalio Telenti / Sean P J Whelan / Herbert W Virgin / Davide Corti / Matteo Samuele Pizzuto / David Veesler /
PubMed AbstractThe SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about ...The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351, and P.1 lineages, harbor frequent mutations within the NTD supersite, suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.
External linksCell / PubMed:33761326 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.2 - 6.5 Å
Structure data

23577

7lxw

EMDB-23577, PDB-7lxw:
SARS-CoV-2 S/S2M11/S2X333 Local Refinement
Method: EM (single particle) / Resolution: 2.8 Å

23578

7lxx

EMDB-23578, PDB-7lxx:
SARS-CoV-2 S/S2M11/S2L28 Local Refinement
Method: EM (single particle) / Resolution: 3.0 Å

23579

7lxy

EMDB-23579, PDB-7lxy:
SARS-CoV-2 S/S2M11/S2X333 Global Refinement
Method: EM (single particle) / Resolution: 2.2 Å

23580

7lxz

EMDB-23580, PDB-7lxz:
SARS-CoV-2 S/S2M11/S2L28 Global Refinement
Method: EM (single particle) / Resolution: 2.6 Å

23581

7ly0

EMDB-23581, PDB-7ly0:
SARS-CoV-2 S/S2M11/S2M28 Local Refinement
Method: EM (single particle) / Resolution: 2.6 Å

23582

7ly2

EMDB-23582, PDB-7ly2:
SARS-CoV-2 S/S2M11/S2M28 Global Refinement
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-23583:
SARS-CoV-2 S/S2M11/S2M24 map
Method: EM (single particle) / Resolution: 6.5 Å

EMDB-23584:
SARS-CoV-2 S/S2X28 map
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-23585:
SARS-CoV-2 S/S2M11/S2X316 map
Method: EM (single particle) / Resolution: 6.0 Å

EMDB-23586:
SARS-CoV-2 S/S2M11/S2L20 map
Method: EM (single particle) / Resolution: 6.3 Å

PDB-7ly3:
Crystal structure of SARS-CoV-2 S NTD bound to S2M28 Fab
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

Chemicals

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

ChemComp-HOH:
WATER / Water

ChemComp-UNX:
Unknown entry

ChemComp-XYL:
Xylitol / Xylitol

ChemComp-SO4:
SULFATE ION / Sulfate

Source
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / VIRAL PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN-IMMUNE SYSTEM complex

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