6BCA

A Complex between PH Domain of LbcRhoGEF (AKAP-Lbc) and Activated RhoA Bound to a GTP Analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of the PH domains from Lbc family of RhoGEFs bound to activated RhoA GTPase.

Chen, Z.Gutowski, S.Sternweis, P.C.

(2018) Data Brief 17: 356-362

  • DOI: https://doi.org/10.1016/j.dib.2018.01.024
  • Primary Citation of Related Structures:  
    6BCA, 6BCB

  • PubMed Abstract: 

    The Pleckstrin homology (PH) domains from the Lbc family of Rho Guanine Nucleotide Exchange Factors (Lbc RhoGEFs) interact with activated Rho family GTPases. All 7 Lbc RhoGEFs associate directly with activated Rho GTPases via their PH domains. However, the binding affinities between the PH domains and the GTPases vary greatly. Here we present two crystal structures at resolutions of 1.4 Å and 2.0 Å of RhoA complexed with the PH domain from p114RhoGEF (PDB access code 6BCB) and AKAP-LbcRhoGEF (PDB access code 6BCA), respectively. These high resolution structures, together with the earlier structures of PDZRhoGEF-PH·RhoA and p190RhoGEF-PH·RhoA complexes, identify a highly conserved interface between the PH domains from Lbc-RhoGEFs and activated Rho GTPases. This manuscript is related to the manuscript titled "Direct Regulation of p190RhoGEF by Activated Rho and Rac GTPases" published in the Journal of Structural Biology.


  • Organizational Affiliation

    Department of Biophysics, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transforming protein RhoAA [auth F],
D [auth C]
185Homo sapiensMutation(s): 0 
Gene Names: RHOAARH12ARHARHO12
UniProt & NIH Common Fund Data Resources
Find proteins for P61586 (Homo sapiens)
Explore P61586 
Go to UniProtKB:  P61586
PHAROS:  P61586
GTEx:  ENSG00000067560 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61586
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
A-kinase anchor protein 13B [auth A],
C [auth B]
151Homo sapiensMutation(s): 0 
Gene Names: AKAP13BRXHT31LBC
UniProt & NIH Common Fund Data Resources
Find proteins for Q12802 (Homo sapiens)
Explore Q12802 
Go to UniProtKB:  Q12802
PHAROS:  Q12802
GTEx:  ENSG00000170776 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12802
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.346α = 91.83
b = 60.525β = 92.97
c = 63.618γ = 90.01
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH-5R01GM031954

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.2: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations