8ENY

Crystal structure of alpha-COPI-WD40 domain R13A 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: 1.90 Å
  • R-Value Free: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

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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: 1.90 Å
  • R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.444α = 90
b = 170.204β = 99.83
c = 71.524γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ACEClick on this verticalbar to view details

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