Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.35 kDa 
• Atom Count: 4613 
• Modelled Residue Count: 550 
• Deposited Residue Count: 558 
• Unique protein chains: 2

4D0N

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

• PDB DOI: 10.2210/pdb4D0N/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-29 Released: 2014-05-21 
• Deposition Author(s): Abdul Azeez, K.R., Shrestha, L., Krojer, T., Allerston, C., von Delft, F., Bountra, C., Arrowsmith, C., Edwards, A.M., Knapp, S., Klussmann, E., Elkins, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

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

• PubMed: 25186459 
• DOI: 10.1042/BJ20140606
• Primary Citation of Related Structures:  
  4D0N, 4D0O


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSFORMING PROTEIN RHOA	A	185	Homo sapiens	Mutation(s): 0  Gene Names: RHOA, ARH12, ARHA, RHO12 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61586 (Homo sapiens) Explore P61586  Go to UniProtKB:  P61586
PHAROS:  P61586

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
A-KINASE ANCHOR PROTEIN 13	B	373	Homo sapiens	Mutation(s): 0  Gene Names: AKAP13, BRX, HT31, LBC
UniProt & NIH Common Fund Data Resources
Find proteins for Q12802 (Homo sapiens) Explore Q12802  Go to UniProtKB:  Q12802
PHAROS:  Q12802

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
SO4	D [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.32	α = 90
b = 86.61	β = 90
c = 116.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-04-29 
• Released Date: 2014-05-21 
Deposition Author(s): Abdul Azeez, K.R., Shrestha, L., Krojer, T., Allerston, C., von Delft, F., Bountra, C., Arrowsmith, C., Edwards, A.M., Knapp, S., Klussmann, E., Elkins, J.M.

Revision History  

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