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Structure paper

TitleStructural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD.
Journal, issue, pagesCell Rep, Vol. 37, Issue 4, Page 109881, Year 2021
Publish dateOct 26, 2021
AuthorsJohn M Errico / Haiyan Zhao / Rita E Chen / Zhuoming Liu / James Brett Case / Meisheng Ma / Aaron J Schmitz / Michael J Rau / James A J Fitzpatrick / Pei-Yong Shi / Michael S Diamond / Sean P J Whelan / Ali H Ellebedy / Daved H Fremont /
PubMed AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has necessitated the rapid development of antibody-based therapies and vaccines as countermeasures. Here, we use cryoelectron ...The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has necessitated the rapid development of antibody-based therapies and vaccines as countermeasures. Here, we use cryoelectron microscopy (cryo-EM) to characterize two protective anti-SARS-CoV-2 murine monoclonal antibodies (mAbs) in complex with the spike protein, revealing similarities between epitopes targeted by human and murine B cells. The more neutralizing mAb, 2B04, binds the receptor-binding motif (RBM) of the receptor-binding domain (RBD) and competes with angiotensin-converting enzyme 2 (ACE2). By contrast, 2H04 binds adjacent to the RBM and does not compete for ACE2 binding. Naturally occurring sequence variants of SARS-CoV-2 and corresponding neutralization escape variants selected in vitro map to our structurally defined epitopes, suggesting that SARS-CoV-2 might evade therapeutic antibodies with a limited set of mutations, underscoring the importance of combination mAb therapeutics. Finally, we show that 2B04 neutralizes SARS-CoV-2 infection by preventing ACE2 engagement, whereas 2H04 reduces host cell attachment without directly disrupting ACE2-RBM interactions, providing distinct inhibitory mechanisms used by RBD-specific mAbs.
External linksCell Rep / PubMed:34655519 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 3.55 Å
Structure data

22748

7k9h

EMDB-22748, PDB-7k9h:
SARS-CoV-2 Spike in complex with neutralizing Fab 2B04 (one up, two down conformation)
Method: EM (single particle) / Resolution: 3.2 Å

22749

7k9i

EMDB-22749, PDB-7k9i:
SARS-CoV-2 Spike RBD in complex with neutralizing Fab 2B04 (local refinement)
Method: EM (single particle) / Resolution: 3.3 Å

22750

7k9j

EMDB-22750, PDB-7k9j:
SARS-CoV-2 Spike in complex with neutralizing Fab 2H04 (three down conformation)
Method: EM (single particle) / Resolution: 3.0 Å

22751

7k9k

EMDB-22751, PDB-7k9k:
SARS-CoV-2 Spike RBD in complex with neutralizing Fab 2H04 (local refinement)
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-22752:
SARS-CoV-2 Spike in complex with neutralizing Fab 2B04 (two up, one down conformation)
Method: EM (single particle) / Resolution: 3.35 Å

EMDB-22753:
SARS-CoV-2 Spike in complex with neutralizing Fab 2H04 (one up, two down conformation)
Method: EM (single particle) / Resolution: 3.55 Å

Chemicals

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

Source
  • severe acute respiratory syndrome coronavirus 2
  • Homo sapiens (human)
  • mus musculus (house mouse)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Neutralizing antibody / ACE2-competitive / Receptor-binding domain / VIRAL PROTEIN-IMMUNE SYSTEM complex / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Complex / ACE2-non-competitive

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