6ZB5 | pdb_00006zb5

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

Validation slider image for 6ZB5

This is version 1.2 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 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. 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
    • School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.

Macromolecule Content 

  • Total Structure Weight: 425.75 kDa 
  • Atom Count: 24,499 
  • Modeled Residue Count: 3,096 
  • Deposited Residue Count: 3,777 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth C],
B,
C [auth A]
1,259Severe 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
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / 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
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

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



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
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary