7NTC | pdb_00007ntc

Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab

• PDB DOI: https://doi.org/10.2210/pdb7NTC/pdb
• EM Map EMD-12587: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2021-03-09 Released: 2021-04-28 
• Deposition Author(s): Rosa, A., Pye, V.E., Nans, A., Cherepanov, P.
• Funding Organization(s): The Francis Crick Institute

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

SARS-CoV-2 can recruit a heme 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., Dos Santos, M.S., 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 7

• PubMed: 33888467 
• DOI: https://doi.org/10.1126/sciadv.abg7607
• Primary Citation Related Structures: 
  7B62, 7NT9, 7NTA, 7NTC


• 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 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.

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Organizational Affiliation: 
• Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK.
Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK.
Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK.
Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK.
Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK.
Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
Flow Cytometry Science and Technology Platform, The Francis Crick Institute, London, UK.
Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK.
Cell Biology of Infection Laboratory, The Francis Crick Institute, London, UK.
Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK.
Cutrale Perioperative and Ageing Group, Imperial College London, London, UK.
Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands.
Weill Medical College of Cornell University, New York, NY, USA.
Advanced Pathogen Diagnostic Unit, University College London Hospitals NHS Foundation Trust, London, UK.
Crick COVID-19 Consortium, The Francis Crick Institute, London, UK.
Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health.
Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, UK.
Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK. [e-mail] [e-mail] [e-mail] [e-mail].
Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK. [e-mail] [e-mail] [e-mail] [e-mail].
Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK. [e-mail] [e-mail] [e-mail] [e-mail].
Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK. [e-mail] [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 497.49 kDa 
• Atom Count: 30,005 
• Modeled Residue Count: 3,698 
• Deposited Residue Count: 4,346 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,287	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 4  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 18		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P008_056 Fab Heavy chain	D [auth H]	253	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
P008_056 Fab Light chain	E [auth L]	232	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], DA [auth d], F [auth V], G [auth D], H [auth E], I [auth F], J [auth G], K [auth I], L [auth J], M [auth K], 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
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLA (Subject of Investigation/LOI)	EA [auth A], OA [auth B]	BILIVERDINE IX ALPHA C33 H34 N4 O6 GWZYPXHJIZCRAJ-SRVCBVSDSA-N
NAG	AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FA [auth A], FB [auth C], GA [auth A], GB [auth C], HA [auth A], HB [auth C], IA [auth A], IB [auth C], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2
MODEL REFINEMENT	PHENIX	1.19rc5-4047

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Rosa, A., Pye, V.E., Nans, A., Cherepanov, P.

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Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	FC001061

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2021-05-05
  Changes: Database references
• Version 1.2: 2021-06-09
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Refinement description, Structure summary