5EFX

Crystal structure of Rho GTPase regulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of hGEF-H1 PH domain provides insight into incapability in phosphoinositide binding

Jiang, Y.Jiang, H.Zhou, S.Meng, B.Liu, Z.J.Ouyang, S.

(2016) Biochem Biophys Res Commun 471: 621-627

  • DOI: https://doi.org/10.1016/j.bbrc.2016.01.150
  • Primary Citation of Related Structures:  
    5EFX

  • PubMed Abstract: 

    The guanine nucleotide exchange factor GEF-H1 (also known as ARHGEF2) is identified as a member of the Dbl family of GEFs. It regulates RhoA-dependent cell signaling pathways and plays important roles in biological processes. GEF-H1 contains an N-terminal zinc finger domain, a Dbl-homologous (DH) domain followed by a Pleckstrin homology (PH) domain, and a C-terminal domain. The specific roles of its PH domain are poorly understood. Here we report the crystal structure of human GEF-H1 PH domain to 2.45 Å resolution. A conserved surface is formed by β8, β9, β10, and it may mediate protein-protein interactions. Although the folding resembles other PH domains that have defined structures, superposition of different PH domains clearly shows that the loop between β6/β7 and the loop between β3/β4 are so close that they will prevent its binding with phosphoinositide due to steric hindrance, and this has been proved by isothermal titration calorimetry (ITC) and thermal shift assay (TSA). Our studies provide a structural framework for further work on the function of GEF-H1.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rho guanine nucleotide exchange factor 2144Homo sapiensMutation(s): 0 
Gene Names: ARHGEF2KIAA0651LFP40
UniProt & NIH Common Fund Data Resources
Find proteins for Q92974 (Homo sapiens)
Explore Q92974 
Go to UniProtKB:  Q92974
PHAROS:  Q92974
GTEx:  ENSG00000116584 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92974
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.948α = 90
b = 81.825β = 90
c = 119.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
Cootmodel building
PHASERphasing
Cootrefinement
REFMACrefinement
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China--

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description