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Structure paper

TitleSARS-CoV-2 can recruit a heme metabolite to evade antibody immunity.
Journal, issue, pagesSci Adv, Vol. 7, Issue 22, Year 2021
Publish dateMay 28, 2021
AuthorsAnnachiara Rosa / Valerie E Pye / Carl Graham / Luke Muir / Jeffrey Seow / Kevin W Ng / Nicola J Cook / Chloe Rees-Spear / Eleanor Parker / Mariana Silva Dos Santos / Carolina Rosadas / Alberto Susana / Hefin Rhys / Andrea Nans / Laura Masino / Chloe Roustan / Evangelos Christodoulou / Rachel Ulferts / Antoni G Wrobel / Charlotte-Eve Short / Michael Fertleman / Rogier W Sanders / Judith Heaney / Moira Spyer / Svend Kjær / Andy Riddell / Michael H Malim / Rupert Beale / James I MacRae / Graham P Taylor / Eleni Nastouli / Marit J van Gils / Peter B Rosenthal / Massimo Pizzato / Myra O McClure / Richard S Tedder / George Kassiotis / Laura E McCoy / Katie J Doores / Peter Cherepanov /
PubMed AbstractThe coronaviral spike is the dominant viral antigen and the target of neutralizing antibodies. We show that SARS-CoV-2 spike binds biliverdin and bilirubin, the tetrapyrrole products of heme ...The coronaviral spike is the dominant viral antigen and the target of neutralizing antibodies. We show that SARS-CoV-2 spike binds biliverdin and bilirubin, the tetrapyrrole products of heme metabolism, with nanomolar affinity. Using cryo-electron microscopy and x-ray crystallography, we mapped the tetrapyrrole interaction pocket to a deep cleft on the spike N-terminal domain (NTD). At physiological concentrations, biliverdin significantly dampened the reactivity of SARS-CoV-2 spike with immune sera and inhibited a subset of neutralizing antibodies. Access to the tetrapyrrole-sensitive epitope is gated by a flexible loop on the distal face of the NTD. Accompanied by profound conformational changes in the NTD, antibody binding requires relocation of the gating loop, which folds into the cleft vacated by the metabolite. Our results indicate that SARS-CoV-2 spike NTD harbors a dominant epitope, access to which can be controlled by an allosteric mechanism that is regulated through recruitment of a metabolite.
External linksSci Adv / PubMed:33888467 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.82 - 3.6 Å
Structure data

12585

7nt9

EMDB-12585, PDB-7nt9:
Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (closed conformation)
Method: EM (single particle) / Resolution: 3.36 Å

12586

7nta

EMDB-12586, PDB-7nta:
Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (one RBD erect)
Method: EM (single particle) / Resolution: 3.5 Å

12587

7ntc

EMDB-12587, PDB-7ntc:
Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab
Method: EM (single particle) / Resolution: 3.6 Å

PDB-7b62:
Crystal structure of SARS-CoV-2 spike protein N-terminal domain in complex with biliverdin
Method: X-RAY DIFFRACTION / Resolution: 1.82 Å

Chemicals

ChemComp-BLA:
BILIVERDINE IX ALPHA

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

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-PGE:
TRIETHYLENE GLYCOL / Polyethylene glycol

ChemComp-1PE:
PENTAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-HOH:
WATER / Water

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / SARSCoV2 / COVID19 / Biliverdin / coronavirus / NTD / green / spike / glycoprotein / S1 / SARS-CoV-2 / Antibody / Fab / epitope

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