6FSF | pdb_00006fsf

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 (Depositor), 0.241 (DCC)
R-Value Work:
0.211 (Depositor), 0.217 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6FSF

This is version 1.2 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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X18005915
Primary Citation 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
Modeled Residue Count: 218
Deposited Residue Count: 269
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.241 (DCC)
R-Value Work: 0.211 (Depositor), 0.217 (DCC)
R-Value Observed: 0.212 (Depositor)

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

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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
Version 1.2: 2024-05-08
Changes: Data collection, Database references

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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.