8ENZ

Crystal structure of alpha-COPI-WD40 domain K15A mutant.

  • Classification: PROTEIN TRANSPORT
  • Organism(s): Schizosaccharomyces pombe
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2022-09-30 Released: 2024-01-31 
  • Deposition Author(s): Dey, D., Hasan, S.S.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


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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
Putative coatomer subunit alpha
A, B, C
337Schizosaccharomyces pombeMutation(s): 1 
UniProt
Find proteins for Q96WV5 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q96WV5 
Go to UniProtKB:  Q96WV5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96WV5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.487α = 90
b = 172.265β = 99.91
c = 71.483γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing

Structure Validation

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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