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Structure paper

TitleStructural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.
Journal, issue, pagesScience, Vol. 375, Issue 6578, Page eabl6251, Year 2022
Publish dateJan 21, 2022
AuthorsKatherine G Nabel / Sarah A Clark / Sundaresh Shankar / Junhua Pan / Lars E Clark / Pan Yang / Adrian Coscia / Lindsay G A McKay / Haley H Varnum / Vesna Brusic / Nicole V Tolan / Guohai Zhou / Michaël Desjardins / Sarah E Turbett / Sanjat Kanjilal / Amy C Sherman / Anand Dighe / Regina C LaRocque / Edward T Ryan / Casey Tylek / Joel F Cohen-Solal / Anhdao T Darcy / Davide Tavella / Anca Clabbers / Yao Fan / Anthony Griffiths / Ivan R Correia / Jane Seagal / Lindsey R Baden / Richelle C Charles / Jonathan Abraham /
PubMed AbstractMany studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we ...Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We demonstrate mechanisms through which the SARS-CoV-2 receptor binding domain (RBD) can tolerate large numbers of simultaneous antibody escape mutations and show that pseudotypes containing up to seven mutations, as opposed to the one to three found in previously studied variants of concern, are more resistant to neutralization by therapeutic antibodies and serum from vaccine recipients. We identify an antibody that binds the RBD core to neutralize pseudotypes for all tested variants but show that the RBD can acquire an N-linked glycan to escape neutralization. Our findings portend continued emergence of escape variants as SARS-CoV-2 adapts to humans.
External linksScience / PubMed:34855508 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.467 - 4.3 Å
Structure data

25209

7sn2

EMDB-25209, PDB-7sn2:
Structure of human SARS-CoV-2 neutralizing antibody C1C-A3 Fab
Method: EM (single particle) / Resolution: 4.3 Å

25210

7sn3

EMDB-25210, PDB-7sn3:
Structure of human SARS-CoV-2 spike glycoprotein trimer bound by neutralizing antibody C1C-A3 Fab (variable region)
Method: EM (single particle) / Resolution: 3.1 Å

PDB-7sn0:
Crystal structure of spike protein receptor binding domain of escape mutant SARS-CoV-2 from immunocompromised patient (d146*) in complex with human receptor ACE2
Method: X-RAY DIFFRACTION / Resolution: 3.08 Å

PDB-7sn1:
Structure of human SARS-CoV-2 neutralizing antibody C1C-A3 Fab
Method: X-RAY DIFFRACTION / Resolution: 1.467 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

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)
KeywordsVIRAL PROTEIN / COVID-19 / SARS-CoV-2 / spike protein / neutralization escape mutant / ACE2 / receptor binding / IMMUNE SYSTEM / neutralizing antibody / neutralization escape / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex

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