8ENW

Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike tail heptapeptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs.

Dey, D.Qing, E.He, Y.Chen, Y.Jennings, B.Cohn, W.Singh, S.Gakhar, L.Schnicker, N.J.Pierce, B.G.Whitelegge, J.P.Doray, B.Orban, J.Gallagher, T.Hasan, S.S.

(2023) Nat Commun 14: 8358-8358

  • DOI: https://doi.org/10.1038/s41467-023-44076-3
  • Primary Citation of Related Structures:  
    8ENS, 8ENW, 8ENX, 8ENY, 8ENZ, 8EO0, 8SZX

  • PubMed Abstract: 

    The spike (S) protein of SARS-CoV-2 is delivered to the virion assembly site in the ER-Golgi Intermediate Compartment (ERGIC) from both the ER and cis-Golgi in infected cells. However, the relevance and modulatory mechanism of this bidirectional trafficking are unclear. Here, using structure-function analyses, we show that S incorporation into virus-like particles (VLP) and VLP fusogenicity are determined by coatomer-dependent S delivery from the cis-Golgi and restricted by S-coatomer dissociation. Although S mimicry of the host coatomer-binding dibasic motif ensures retrograde trafficking to the ERGIC, avoidance of the host-like C-terminal acidic residue is critical for S-coatomer dissociation and therefore incorporation into virions or export for cell-cell fusion. Because this C-terminal residue is the key determinant of SARS-CoV-2 assembly and fusogenicity, our work provides a framework for the export of S protein encoded in genetic vaccines for surface display and immune activation.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit beta'
A, B
302Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for G2WDW6 (Saccharomyces cerevisiae (strain Kyokai no. 7 / NBRC 101557))
Explore G2WDW6 
Go to UniProtKB:  G2WDW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2WDW6
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Clientized spike tail peptide
C, D
7Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth B],
N [auth B],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.711α = 81.24
b = 46.012β = 81.52
c = 84.319γ = 69.01
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA134274
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM150187

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release