1LV0 | pdb_00001lv0

Crystal structure of the Rab effector guanine nucleotide dissociation inhibitor (GDI) in complex with a geranylgeranyl (GG) peptide

• PDB DOI: https://doi.org/10.2210/pdb1LV0/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-23 Released: 2003-08-05 
• Deposition Author(s): An, Y., Shao, Y., Alory, C., Matteson, J., Sakisaka, T., Chen, W., Gibbs, R.A., Wilson, I.A., Balch, W.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Geranylgeranyl switching regulates GDI-Rab GTPase recycling.

An, Y., Shao, Y., Alory, C., Matteson, J., Sakisaka, T., Chen, W., Gibbs, R.A., Wilson, I.A., Balch, W.E.

(2003) Structure 11: 347-357

• PubMed: 12623022 
• DOI: https://doi.org/10.1016/s0969-2126(03)00034-0
• Primary Citation Related Structures: 
  1LV0


• PubMed Abstract: 
  

  Rab GTPases, key regulators of membrane targeting and fusion, require the covalent attachment of geranylgeranyl lipids to their C terminus for function. To elucidate the role of lipid in Rab recycling, we have determined the crystal structure of Rab guanine nucleotide dissociation inhibitor (alphaGDI) in complex with a geranylgeranyl (GG) ligand (H(2)N-Cys-(S-GG)-OMe). The lipid is bound beneath the Rab binding platform in a shallow hydrophobic groove. Mutation of the binding pocket in the brain-specific alphaGDI leads to mental retardation. Strikingly, lipid binding acts through a conserved allosteric switching mechanism to promote release of the GDI-Rab[GDP] complex from the membrane.

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Organizational Affiliation: 
• The Scripps Research Institute, Department of Cell Biology, 10550 North Torrey Pines Road, La Jolla, CA 92130, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.46 kDa 
• Atom Count: 3,834 
• Modeled Residue Count: 433 
• Deposited Residue Count: 449 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAB GDP disossociation inhibitor alpha	A	449	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P21856 (Bos taurus) Explore P21856  Go to UniProtKB:  P21856

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GER	E [auth A]	GERAN-8-YL GERAN C20 H34 HSOYJGBJQAKCNA-CAIKYXSQSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.249 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.23	α = 90
b = 42.861	β = 103.53
c = 89.104	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-05 
Deposition Author(s): An, Y., Shao, Y., Alory, C., Matteson, J., Sakisaka, T., Chen, W., Gibbs, R.A., Wilson, I.A., Balch, W.E.

Revision History  

• Version 1.0: 2003-08-05
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description