3Q72

Crystal Structure of Rad G-domain-GTP Analog Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

RGK Family G-Domain:GTP Analog Complex Structures and Nucleotide-Binding Properties.

Sasson, Y.Navon-Perry, L.Huppert, D.Hirsch, J.A.

(2011) J Mol Biol 413: 372-389

  • DOI: 10.1016/j.jmb.2011.08.017
  • Primary Citation of Related Structures:  
    3Q72, 3Q7Q, 3Q85, 3Q7P

  • PubMed Abstract: 
  • The RGK family of small G-proteins, including Rad, Gem, Rem1, and Rem2, is inducibly expressed in various mammalian tissues and interacts with voltage-dependent calcium channels and Rho kinase. Many questions remain regarding their physiological roles an ...

    The RGK family of small G-proteins, including Rad, Gem, Rem1, and Rem2, is inducibly expressed in various mammalian tissues and interacts with voltage-dependent calcium channels and Rho kinase. Many questions remain regarding their physiological roles and molecular mechanism. Previous crystallographic studies reported RGK G-domain:guanosine di-phosphate structures. To test whether RGK proteins undergo a nucleotide-induced conformational change, we determined the crystallographic structures of Rad:GppNHp and Rem2:GppNHp to 1.7 and 1.8 Å resolutions, respectively. Also, we characterized the nucleotide-binding properties and conformations for Gem, Rad, and several structure-based mutants using fluorescence spectroscopy. The results suggest that RGK G-proteins may not behave as Ras-like canonical nucleotide-induced molecular switches. Further, the RGK proteins have differing structures and nucleotide-binding properties, which may have implications for their varied action on effectors.


    Organizational Affiliation

    Department of Biochemistry, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding protein RAD AB166Homo sapiensMutation(s): 0 
Gene Names: RRADRAD
Find proteins for P55042 (Homo sapiens)
Explore P55042 
Go to UniProtKB:  P55042
NIH Common Fund Data Resources
PHAROS:  P55042
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GNPKd :  1574   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.084α = 90
b = 39.084β = 90
c = 154.671γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references