8ENY | pdb_00008eny

Crystal structure of alpha-COPI-WD40 domain R13A mutant.

• PDB DOI: https://doi.org/10.2210/pdb8ENY/pdb

• 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)

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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), 0.179 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

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

• PubMed: 38102143 
• DOI: https://doi.org/10.1038/s41467-023-44076-3
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA.
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA.
Department of Internal Medicine, Hematology Division, Washington University School of Medicine, St. Louis, MO, 63110, USA.
Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
Protein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
PAQ Therapeutics, Burlington, MA, 01803, USA.
Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. [e-mail].
University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD, 21201, USA. [e-mail].
Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Rockville, MD, 20850, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.49 kDa 
• Atom Count: 7,928 
• Modeled Residue Count: 917 
• Deposited Residue Count: 1,011 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative coatomer subunit alpha	A, B, C	337	Schizosaccharomyces pombe	Mutation(s): 1
UniProt
Find proteins for Q96WV5 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q96WV5  Go to UniProtKB:  Q96WV5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACE (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N

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), 0.179 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.444	α = 90
b = 170.204	β = 99.83
c = 71.524	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Dey, D., Hasan, S.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30CA134274
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM150187

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary