8SZX

Crystal structure of b'-WD40 Lys17Ala mutant

  • Classification: PROTEIN TRANSPORT
  • Organism(s): Saccharomyces cerevisiae
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2023-05-30 Released: 2024-02-14 
  • 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: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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): 1 
Gene Names: EC1118_1G1_1453g
UniProt
Find proteins for P41811 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41811 
Go to UniProtKB:  P41811
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41811
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.189α = 90
b = 158.189β = 90
c = 47.567γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing

Structure Validation

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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: 2024-02-14
    Type: Initial release