4D0N

AKAP13 (AKAP-Lbc) RhoGEF domain in complex with RhoA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The Crystal Structure of the Rhoa : Akap-Lbc Dh-Ph Domain Complex.

Abdul Azeez, K.R., Knapp, S., Fernandes, J.M.P., Klussmann, E., Elkins, J.M.

(2014) Biochem.J. 464: 231

  • DOI: 10.1042/BJ20140606
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The RhoGEF (Rho GTPase guanine-nucleotide-exchange factor) domain of AKAP-Lbc (A-kinase-anchoring protein-Lbc, also known as AKAP13) catalyses nucleotide exchange on RhoA and is involved in the development of cardiac hypertrophy. The RhoGEF activity ...

    The RhoGEF (Rho GTPase guanine-nucleotide-exchange factor) domain of AKAP-Lbc (A-kinase-anchoring protein-Lbc, also known as AKAP13) catalyses nucleotide exchange on RhoA and is involved in the development of cardiac hypertrophy. The RhoGEF activity of AKAP-Lbc has also been implicated in cancer. We have determined the X-ray crystal structure of the complex between RhoA-GDP and the AKAP-Lbc RhoGEF [DH (Dbl-homologous)-PH (pleckstrin homology)] domain to 2.1 Å (1 Å = 0.1 nm) resolution. The structure reveals important differences compared with related RhoGEF proteins such as leukaemia-associated RhoGEF. Nucleotide-exchange assays comparing the activity of the DH-PH domain to the DH domain alone showed no role for the PH domain in nucleotide exchange, which is explained by the RhoA-AKAP-Lbc structure. Comparison with a structure of the isolated AKAP-Lbc DH domain revealed a change in conformation of the N-terminal 'GEF switch' region upon binding to RhoA. Isothermal titration calorimetry showed that AKAP-Lbc has only micromolar affinity for RhoA, which combined with the presence of potential binding pockets for small molecules on AKAP-Lbc, raises the possibility of targeting AKAP-Lbc with GEF inhibitors.

    Organizational Affiliation: 

    *Structural Genomics Consortium, Oxford University, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSFORMING PROTEIN RHOA
A
185Homo sapiensMutation(s): 0 
Gene Names: RHOA (ARH12, ARHA, RHO12)
EC: 3.6.5.2
Find proteins for P61586 (Homo sapiens)
Go to Gene View: RHOA
Go to UniProtKB:  P61586
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
A-KINASE ANCHOR PROTEIN 13
B
373Homo sapiensMutation(s): 0 
Gene Names: AKAP13 (BRX, HT31, LBC)
Find proteins for Q12802 (Homo sapiens)
Go to Gene View: AKAP13
Go to UniProtKB:  Q12802
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.320α = 90.00
b = 86.610β = 90.00
c = 116.820γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-09-17
    Type: Database references
  • Version 1.2: 2014-11-26
    Type: Database references