6FSF

Crystal structure of the tandem PX-PH-domains of Bem3 from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb6FSF/pdb

Classification: ENDOCYTOSIS
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-19 Released: 2018-05-02
Deposition Author(s): Ali, I., Eu, S., Koch, D., Bleimling, N., Goody, R.S., Mueller, M.P.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.234
R-Value Work: 0.211
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the tandem PX-PH domains of Bem3 from Saccharomyces cerevisiae.

Ali, I., Eu, S., Koch, D., Bleimling, N., Goody, R.S., Muller, M.P.

(2018) Acta Crystallogr F Struct Biol Commun 74: 315-321

PubMed: 29718000 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X18005915
Primary Citation of Related Structures:
6FSF

PubMed Abstract:
The structure of the tandem lipid-binding PX and pleckstrin-homology (PH) domains of the Cdc42 GTPase-activating protein Bem3 from Saccharomyces cerevisiae (strain S288c) has been determined to a resolution of 2.2 Å (R _work = 21.1%, R _free = 23.4%). It shows that the domains adopt a relative orientation that enables them to simultaneously bind to a membrane and suggests possible cooperativity in membrane binding.

Organizational Affiliation

Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 30.74 kDa
Atom Count: 1,808
Modelled Residue Count: 218
Deposited Residue Count: 269
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase-activating protein BEM3	A	269	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: BEM3, YPL115C, LPH12C
UniProt
Find proteins for P32873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32873 Go to UniProtKB: P32873
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32873
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.234
R-Value Work: 0.211
R-Value Observed: 0.212
Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.37	α = 90
b = 85.37	β = 90
c = 63.97	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	DFG/ANR grant GO 284/8-1
German Research Foundation	Germany	SFB 642

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2018-05-09
Changes: Data collection, Database references

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.