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Structure paper

TitleStructural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 311, Year 2023
Publish dateJan 19, 2023
AuthorsKuan-Ying A Huang / Xiaorui Chen / Arpita Mohapatra / Hong Thuy Vy Nguyen / Lisa Schimanski / Tiong Kit Tan / Pramila Rijal / Susan K Vester / Rory A Hills / Mark Howarth / Jennifer R Keeffe / Alexander A Cohen / Leesa M Kakutani / Yi-Min Wu / Md Shahed-Al-Mahmud / Yu-Chi Chou / Pamela J Bjorkman / Alain R Townsend / Che Ma /
PubMed AbstractAntibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural ...Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the "down" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.
External linksNat Commun / PubMed:36658148 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.13 - 4.28 Å
Structure data

34806

8hhx

EMDB-34806, PDB-8hhx:
SARS-CoV-2 Delta Spike in complex with FP-12A
Method: EM (single particle) / Resolution: 3.62 Å

34807

8hhy

EMDB-34807, PDB-8hhy:
SARS-CoV-2 Delta Spike in complex with IS-9A
Method: EM (single particle) / Resolution: 2.77 Å

34808

8hhz

EMDB-34808, PDB-8hhz:
SARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A
Method: EM (single particle) / Resolution: 4.28 Å

PDB-7yck:
Crystal structure of SARS-CoV-2 Spike RBD in complex with FP-12A Fab
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-7ycl:
Crystal structure of SARS-CoV-2 Spike RBD in complex with IS-9A Fab
Method: X-RAY DIFFRACTION / Resolution: 2.13 Å

PDB-7ycn:
Crystal structure of SARS-CoV-2 Spike RBD in complex with IY-2A Fab
Method: X-RAY DIFFRACTION / Resolution: 2.85 Å

Chemicals

ChemComp-HOH:
WATER / Water

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

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / SARS-CoV-2 / Spike / RBD / class 4 / VIRAL PROTEIN-IMMUNE SYSTEM complex / Delta variant / monoclonal antibody / Fab / FP-12A / VIRAL PROTEIN / IS-9A / Omicron variant / BA.1 / IY-2A

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