7S23 | pdb_00007s23

Crystal structure of alpha-COP-WD40 domain, Y139A mutant

PDB DOI: https://doi.org/10.2210/pdb7S23/pdb

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

Deposited: 2021-09-03 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.184 (Depositor), 0.180 (DCC)
R-Value Work:
0.140 (Depositor), 0.140 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 116.42 kDa
Atom Count: 8,425
Modeled Residue Count: 926
Deposited Residue Count: 1,014
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit alpha	A, B, C	338	Schizosaccharomyces pombe	Mutation(s): 2
UniProt
Find proteins for Q96WV5 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q96WV5 Go to UniProtKB: Q96WV5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96WV5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.184 (Depositor), 0.180 (DCC)
R-Value Work: 0.140 (Depositor), 0.140 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.315	α = 90
b = 171.553	β = 99.71
c = 71.281	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-02-16

Deposition Author(s):

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 (Full details and data files)

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
Version 1.3: 2024-10-09
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.