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: 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 glycoproteinC [auth A],
B,
A [auth C]
1259Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
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 

Structure Validation

View Full Validation Report




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