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Structure paper

TitleMolecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response.
Journal, issue, pagesStructure, Vol. 31, Issue 7, Page 801-811.e5, Year 2023
Publish dateJul 6, 2023
AuthorsAnamika Patel / Sanjeev Kumar / Lilin Lai / Chennareddy Chakravarthy / Rajesh Valanparambil / Elluri Seetharami Reddy / Kamalvishnu Gottimukkala / Prashant Bajpai / Dinesh Ravindra Raju / Venkata Viswanadh Edara / Meredith E Davis-Gardner / Susanne Linderman / Kritika Dixit / Pragati Sharma / Grace Mantus / Narayanaiah Cheedarla / Hans P Verkerke / Filipp Frank / Andrew S Neish / John D Roback / Carl W Davis / Jens Wrammert / Rafi Ahmed / Mehul S Suthar / Amit Sharma / Kaja Murali-Krishna / Anmol Chandele / Eric A Ortlund /
PubMed AbstractUnderstanding the molecular features of neutralizing epitopes is important for developing vaccines/therapeutics against emerging SARS-CoV-2 variants. We describe three monoclonal antibodies (mAbs) ...Understanding the molecular features of neutralizing epitopes is important for developing vaccines/therapeutics against emerging SARS-CoV-2 variants. We describe three monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during the first wave of the pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, poorly neutralized Beta, and failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these mAbs in complex with trimeric spike protein showed that all three mAbs bivalently bind spike with two mAbs targeting class 1 and one targeting a class 4 receptor binding domain epitope. The immunogenetic makeup, structure, and function of these mAbs revealed specific molecular interactions associated with the potent multi-variant binding/neutralization efficacy. This knowledge shows how mutational combinations can affect the binding or neutralization of an antibody, which in turn relates to the efficacy of immune responses to emerging SARS-CoV-2 escape variants.
External linksStructure / PubMed:37167972 / PubMed Central
MethodsEM (single particle)
Resolution3.82 - 4.4 Å
Structure data

26263

7u0q

EMDB-26263, PDB-7u0q:
SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-02
Method: EM (single particle) / Resolution: 3.86 Å

26267

7u0x

EMDB-26267, PDB-7u0x:
SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-13
Method: EM (single particle) / Resolution: 3.82 Å

26656

7uow

EMDB-26656, PDB-7uow:
SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 034_32
Method: EM (single particle) / Resolution: 4.4 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-Cov2 6P spike protein / immune complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex

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