3Q72 | pdb_00003q72

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 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

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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 Biology 413: 372-389

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

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 37.64 kDa 
  • Atom Count: 2,425 
  • Modeled Residue Count: 283 
  • Deposited Residue Count: 332 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTP-binding protein RAD
A, B
166Homo sapiensMutation(s): 0 
Gene Names: RRAD, RAD
UniProt & NIH Common Fund Data Resources
Find proteins for P55042 (Homo sapiens)
Explore P55042 
Go to UniProtKB:  P55042
PHAROS:  P55042
GTEx:  ENSG00000166592 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55042
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.225 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations