3CX8

Crystal Structure of PDZRhoGEF rgRGS Domain in a Complex with Galpha-13 Bound to GTP-gamma-S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Recognition of the Activated States of Galpha13 by the rgRGS Domain of PDZRhoGEF.

Chen, Z.Singer, W.D.Danesh, S.M.Sternweis, P.C.Sprang, S.R.

(2008) Structure 16: 1532-1543

  • DOI: 10.1016/j.str.2008.07.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • G12 class heterotrimeric G proteins stimulate RhoA activation by RGS-RhoGEFs. However, p115RhoGEF is a GTPase Activating Protein (GAP) toward Galpha13, whereas PDZRhoGEF is not. We have characterized the interaction between the PDZRhoGEF rgRGS domain ...

    G12 class heterotrimeric G proteins stimulate RhoA activation by RGS-RhoGEFs. However, p115RhoGEF is a GTPase Activating Protein (GAP) toward Galpha13, whereas PDZRhoGEF is not. We have characterized the interaction between the PDZRhoGEF rgRGS domain (PRG-rgRGS) and the alpha subunit of G13 and have determined crystal structures of their complexes in both the inactive state bound to GDP and the active states bound to GDP*AlF (transition state) and GTPgammaS (Michaelis complex). PRG-rgRGS interacts extensively with the helical domain and the effector-binding sites on Galpha13 through contacts that are largely conserved in all three nucleotide-bound states, although PRG-rgRGS has highest affinity to the Michaelis complex. An acidic motif in the N terminus of PRG-rgRGS occupies the GAP binding site of Galpha13 and is flexible in the GDP*AlF complex but well ordered in the GTPgammaS complex. Replacement of key residues in this motif with their counterparts in p115RhoGEF confers GAP activity.


    Organizational Affiliation

    Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein alpha-13 subunit
A
338Mus musculusMutation(s): 0 
Gene Names: Gna13 (Gna-13)
Find proteins for P27601 (Mus musculus)
Go to UniProtKB:  P27601
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rho guanine nucleotide exchange factor 11
B
203Rattus norvegicusMutation(s): 0 
Gene Names: Arhgef11
Find proteins for Q9ES67 (Rattus norvegicus)
Go to UniProtKB:  Q9ES67
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GSP
Query on GSP

Download SDF File 
Download CCD File 
A
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.109α = 90.00
b = 66.117β = 90.00
c = 152.521γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-3000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
CNSrefinement
DENZOdata reduction
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-04-23 
  • Released Date: 2008-10-28 
  • Deposition Author(s): Sprang, S.R., Chen, Z.

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description