3CX7

Crystal Structure of PDZRhoGEF rgRGS Domain in a Complex with Galpha-13 Bound to GDP-AlF4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.264 

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Ligand Structure Quality Assessment 


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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:  
    3CX6, 3CX7, 3CX8

  • 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 (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) ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine Nucleotide-Binding Protein Galpha 13A338Mus musculusMutation(s): 0 
Gene Names: Gna13Gna-13
UniProt & NIH Common Fund Data Resources
Find proteins for P27601 (Mus musculus)
Explore P27601 
Go to UniProtKB:  P27601
IMPC:  MGI:95768
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27601
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate Transporter Associated Protein 48B203Rattus norvegicusMutation(s): 0 
Gene Names: Arhgef11
UniProt
Find proteins for Q9ES67 (Rattus norvegicus)
Explore Q9ES67 
Go to UniProtKB:  Q9ES67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ES67
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ALF
Query on ALF

Download Ideal Coordinates CCD File 
D [auth A]TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.264 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.952α = 90
b = 66.371β = 90
c = 151.19γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance