1GND | pdb_00001gnd

GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM

• PDB DOI: https://doi.org/10.2210/pdb1GND/pdb

• Classification: GTPASE ACTIVATION
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-07-10 Released: 1997-02-12 
• Deposition Author(s): Schalk, I., Zeng, K., Wu, S.-K., Stura, E.A., Metteson, J., Huang, M., Tandon, A., Wilson, I.A., Balch, W.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.275 (Depositor) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Structure and mutational analysis of Rab GDP-dissociation inhibitor.

Schalk, I., Zeng, K., Wu, S.K., Stura, E.A., Matteson, J., Huang, M., Tandon, A., Wilson, I.A., Balch, W.E.

(1996) Nature 381: 42-48

• PubMed: 8609986 
• DOI: https://doi.org/10.1038/381042a0
• Primary Citation Related Structures: 
  1GND


• PubMed Abstract: 
  

  The crystal structure of the bovine alpha-isoform of Rab GDP-dissociation inhibitor (GDI), which functions in vesicle-membrane transport to recycle and regulate Rab GTPases, has been determined to a resolution of 1.81 A. GDI is constructed of two main structural units, a large complex multisheet domain I and a smaller alpha-helical domain II. The structural organization of domain I is surprisingly closely related to FAD-containing monooxygenases and oxidases. Sequence-conserved regions common to GDI and the choroideraemia gene product, which delivers Rab to catalytic subunits of Rab geranylgeranyltransferase II, are clustered on one face of the molecule. The two most sequence-conserved regions, which form a compact structure at the apex of GDI, are shown by site-directed mutagenesis to play a critical role in the binding of Rab proteins.

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Organizational Affiliation: 
• Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 50.62 kDa 
• Atom Count: 3,823 
• Modeled Residue Count: 430 
• Deposited Residue Count: 447 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR	A	447	Bos taurus	Mutation(s): 0  Gene Names: BOVGDI
UniProt
Find proteins for P21856 (Bos taurus) Explore P21856  Go to UniProtKB:  P21856

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.275 (Depositor) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.8	α = 90
b = 43.5	β = 104.5
c = 63.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-02-12 
Deposition Author(s): Schalk, I., Zeng, K., Wu, S.-K., Stura, E.A., Metteson, J., Huang, M., Tandon, A., Wilson, I.A., Balch, W.E.

Revision History  

• Version 1.0: 1997-02-12
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Other