1D5T

GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.209 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A new functional domain of guanine nucleotide dissociation inhibitor (alpha-GDI) involved in Rab recycling.

Luan, P.Heine, A.Zeng, K.Moyer, B.Greasely, S.E.Kuhn, P.Balch, W.E.Wilson, I.A.

(2000) Traffic 1: 270-281

  • DOI: https://doi.org/10.1034/j.1600-0854.2000.010309.x
  • Primary Citation of Related Structures:  
    1D5T

  • PubMed Abstract: 

    Guanine nucleotide dissociation inhibitor (GDI) is a 55-kDa protein that functions in vesicular membrane transport to recycle Rab GTPases. We have now determined the crystal structure of bovine alpha-GDI at ultra-high resolution (1.04 A). Refinement at this resolution highlighted a region with high mobility of its main-chain residues. This corresponded to a surface loop in the primarily alpha-helical domain II at the base of alpha-GDI containing the previously uncharacterized sequence-conserved region (SCR) 3A. Site-directed mutagenesis showed that this mobile loop plays a crucial role in binding of GDI to membranes and extraction of membrane-bound Rab. This domain, referred to as the mobile effector loop, in combination with Rab-binding residues found in the multi-sheet domain I at the apex of alpha-GDI may provide flexibility for recycling of diverse Rab GTPases. We propose that conserved residues in domains I and II synergize to form the functional face of GDI, and that domain II mediates a critical step in Rab recycling during vesicle fusion.


  • Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR433Bos taurusMutation(s): 0 
UniProt
Find proteins for P21856 (Bos taurus)
Explore P21856 
Go to UniProtKB:  P21856
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21856
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.209 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.29α = 90
b = 42.74β = 104.55
c = 61.78γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 1.5: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description