8CUK

X-ray Structure of the WD40 domain of HOPS subunit Vps11 from Yeast

PDB DOI: https://doi.org/10.2210/pdb8CUK/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-17 Released: 2022-05-25
Deposition Author(s): Port, S.A., Baker, R.W., Jeffrey, P.D., Hughson, F.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.234
R-Value Work: 0.174
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

X-ray Structure of the WD40 domain of HOPS subunit Vps11 from Yeast

Port, S.A., Baker, R.W., Jeffrey, P.D., Hughson, F.M.

To be published.

Macromolecule Content

Total Structure Weight: 127.07 kDa
Atom Count: 8,288
Modelled Residue Count: 994
Deposited Residue Count: 1,137
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase PEP5	A, B, C	379	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: PEP5, END1, VAM1, VPL9, VPS11, VPT11, YMR231W, YM9959.13 EC: 2.3.2.27
UniProt
Find proteins for P12868 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P12868 Go to UniProtKB: P12868
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12868
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.234
R-Value Work: 0.174
R-Value Observed: 0.177
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.084	α = 90
b = 113.159	β = 90
c = 129.758	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXCD	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM071574

Revision History (Full details and data files)

Version 1.0: 2022-05-25
Type: Initial release
Version 1.1: 2024-02-14
Changes: Data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.