7NTA

Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (one RBD erect)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

SARS-CoV-2 can recruit a haem metabolite to evade antibody immunity.

Rosa, A.Pye, V.E.Graham, C.Muir, L.Seow, J.Ng, K.W.Cook, N.J.Rees-Spear, C.Parker, E.Silva Dos Santos, M.Rosadas, C.Susana, A.Rhys, H.Nans, A.Masino, L.Roustan, C.Christodoulou, E.Ulferts, R.Wrobel, A.G.Short, C.E.Fertleman, M.Sanders, R.W.Heaney, J.Spyer, M.Kjaer, S.Riddell, A.Malim, M.H.Beale, R.MacRae, J.I.Taylor, G.P.Nastouli, E.van Gils, M.J.Rosenthal, P.B.Pizzato, M.McClure, M.O.Tedder, R.S.Kassiotis, G.McCoy, L.E.Doores, K.J.Cherepanov, P.

(2021) Sci Adv 

  • DOI: 10.1126/sciadv.abg7607
  • Primary Citation of Related Structures:  
    7B62, 7NT9, 7NTC, 7NTA

  • PubMed Abstract: 
  • 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 haem 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) ...

    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 haem 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 the recruitment of a metabolite.


    Organizational Affiliation

    Department of Infectious Disease, St-Mary's Campus, Imperial College London, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinC [auth A], A [auth B], B [auth C]1287Severe acute respiratory syndrome coronavirus 2Mutation(s): 4 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a], BA [auth b], D [auth V], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H]
AA [auth a], BA [auth b], D [auth V], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N], P [auth O], Q [auth P], R [auth Q], S [auth R], T [auth S], U [auth T], V [auth U], W, X, Y, Z
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLA
Query on BLA

Download Ideal Coordinates CCD File 
CA [auth B], KA [auth C], VA [auth A]BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth A] , BB [auth A] , CB [auth A] , DA [auth B] , DB [auth A] , EA [auth B] , EB [auth A] , FA [auth B] , 
AB [auth A],  BB [auth A],  CB [auth A],  DA [auth B],  DB [auth A],  EA [auth B],  EB [auth A],  FA [auth B],  FB [auth A],  GA [auth B],  HA [auth B],  IA [auth B],  JA [auth B],  LA [auth C],  MA [auth C],  NA [auth C],  OA [auth C],  PA [auth C],  QA [auth C],  RA [auth C],  SA [auth C],  TA [auth C],  UA [auth C],  WA [auth A],  XA [auth A],  YA [auth A],  ZA [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomFC001061

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references