7S16

Crystal structure of alpha-COP-WD40 domain R57A mutant

• PDB DOI: https://doi.org/10.2210/pdb7S16/pdb

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


• Deposited: 2021-09-01 Released: 2022-02-16 
• Deposition Author(s): Dey, D., Singh, S., Khan, S., Martin, M., Schnicker, N., Gakhar, L., Pierce, B., Hasan, S.S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.159 
• R-Value Work: 0.135 
• R-Value Observed: 0.136 

Starting Model: experimental

Literature

An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking

Dey, D., Singh, S., Khan, S., Martin, M., Schnicker, N.J., Gakhar, L., Pierce, B.G., Hasan, S.S.

(2022) Commun Biol 5: 115

• DOI: https://doi.org/10.1038/s42003-022-03063-y

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.84 kDa 
• Atom Count: 2,953 
• Modelled Residue Count: 322 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit alpha	A	338	Schizosaccharomyces pombe	Mutation(s): 2
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
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.159 
• R-Value Work: 0.135 
• R-Value Observed: 0.136 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.868	α = 90
b = 56.712	β = 99.37
c = 70.548	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-16 
Deposition Author(s): Dey, D., Singh, S., Khan, S., Martin, M., Schnicker, N., Gakhar, L., Pierce, B., 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 Cancer Institute (NIH/NCI)	United States	P30CA086862

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release
  
• Version 1.1: 2022-03-02
  Changes: Author supporting evidence
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description