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Structure paper

TitleThe SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 2734, Year 2024
Publish dateMar 28, 2024
AuthorsDaming Zhou / Piyada Supasa / Chang Liu / Aiste Dijokaite-Guraliuc / Helen M E Duyvesteyn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Wanwisa Dejnirattisai / Nigel Temperton / Paul Klenerman / Susanna J Dunachie / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
PubMed AbstractUnder pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed ...Under pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response.
External linksNat Commun / PubMed:38548763 / PubMed Central
MethodsEM (single particle)
Resolution2.2 - 2.7 Å
Structure data

16680

8cin

EMDB-16680, PDB-8cin:
BA.4/5-5 FAB IN COMPLEX WITH SARS-COV-2 BA.4 SPIKE GLYCOPROTEIN
Method: EM (single particle) / Resolution: 2.7 Å

18807

8r1c

EMDB-18807: SD1-2 fab in complex with SARS-COV-2 BA.12.1 Spike Glycoprotein.
PDB-8r1c: SD1-2 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein
Method: EM (single particle) / Resolution: 2.2 Å

18808

8r1d

EMDB-18808, PDB-8r1d:
SD1-3 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein
Method: EM (single particle) / Resolution: 2.37 Å

Chemicals

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

ChemComp-HOH:
WATER / Water

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
  • enterobacteria phage t4 (virus)
KeywordsVIRAL PROTEIN / SARS-CoV2 / spike / glycoprotein / coronavirus / antibody / fab / BA.4 / BA.5 / BA.4/5-5 / cross-protective / omicron variant / vaccine / therapeutic / complex / neutralising / convalescent sera / immune system / SARS-CoV-2 / SD1 domain / neutralisingm convalescent sera / SD1-2 / BA.2.12.1 / virus / BA.2.86 / SD1-3

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