6ZB5

SARS CoV-2 Spike protein, Closed conformation, C3 symmetry

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 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

Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein.

Toelzer, C., Gupta, K., Yadav, S.K.N., Borucu, U., Davidson, A.D., Kavanagh Williamson, M., Shoemark, D.K., Garzoni, F., Staufer, O., Milligan, R., Capin, J., Mulholland, A.J., Spatz, J., Fitzgerald, D., Berger, I., Schaffitzel, C.

(2020) Science 370: 725-730

  • DOI: https://doi.org/10.1126/science.abd3255
  • Primary Citation of Related Structures:  
    6ZB4, 6ZB5

  • PubMed Abstract: 

    • Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents a global crisis. Key to SARS-CoV-2 therapeutic development is unraveling the mechanisms that drive high infectivity, broad tissue tropism, and severe pathology ...

    Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents a global crisis. Key to SARS-CoV-2 therapeutic development is unraveling the mechanisms that drive high infectivity, broad tissue tropism, and severe pathology. Our 2.85-angstrom cryo-electron microscopy structure of SARS-CoV-2 spike (S) glycoprotein reveals that the receptor binding domains tightly bind the essential free fatty acid linoleic acid (LA) in three composite binding pockets. A similar pocket also appears to be present in the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). LA binding stabilizes a locked S conformation, resulting in reduced angiotensin-converting enzyme 2 (ACE2) interaction in vitro . In human cells, LA supplementation synergizes with the COVID-19 drug remdesivir, suppressing SARS-CoV-2 replication. Our structure directly links LA and S, setting the stage for intervention strategies that target LA binding by SARS-CoV-2.

    Organizational Affiliation: 

    Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave., Bristol BS8 1TQ, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinA [auth C],
B,
C [auth A]		1,259Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD, E, F 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EIC (Subject of Investigation/LOI)
Query on EIC
Download Ideal Coordinates CCD File 
M [auth C],
V [auth B],
W [auth B]		LINOLEIC ACID
C18 H32 O2
OYHQOLUKZRVURQ-HZJYTTRNSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
CA [auth A],
G [auth C],
H [auth C],
AA [auth A],
BA [auth A],
CA [auth A],
G [auth C],
H [auth C],
I [auth C],
J [auth C],
K [auth C],
L [auth C],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
X [auth A],
Y [auth A],
Z [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: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P000940/1
Wellcome TrustUnited Kingdom202904/Z/16/Z
Wellcome TrustUnited Kingdom206181/Z/17/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L01386X/1
Wellcome TrustUnited Kingdom210701/Z/18/Z
Wellcome TrustUnited Kingdom106115/Z/14/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R000484/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references