Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75448.65 
• Atom Count: 5214 
• Residue Count: 659 
• Unique protein chains: 2

1UKV

Structure of RabGDP-dissociation inhibitor in complex with prenylated YPT1 GTPase

• DOI: 10.2210/pdb1UKV/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2003-09-01 Released: 2004-09-01 
• Deposition Author(s): Rak, A., Pylypenko, O., Durek, T., Watzke, A., Kushnir, S., Brunsveld, L., Waldmann, H., Goody, R.S., Alexandrov, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.216 
• R-Value Work: 0.192 

Literature

Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase

Rak, A., Pylypenko, O., Durek, T., Watzke, A., Kushnir, S., Brunsveld, L., Waldmann, H., Goody, R.S., Alexandrov, K.

(2003) Science 302: 646-650

• PubMed: 14576435 
• DOI: 10.1126/science.1087761


• PubMed Abstract: 
  

Rab/Ypt guanosine triphosphatases (GTPases) represent a family of key membrane traffic regulators in eukaryotic cells whose function is governed by the guanosine diphosphate (GDP) dissociation inhibitor (RabGDI). Using a combination of chemical synthesis and protein engineering, we generated and crystallized the monoprenylated Ypt1:RabGDI complex. The structure of the complex was solved to 1.5 angstrom resolution and provides a structural basis for the ability of RabGDI to inhibit the release of nucleotide by Rab proteins. Isoprenoid binding requires a conformational change that opens a cavity in the hydrophobic core of its domain II. Analysis of the structure provides a molecular basis for understanding a RabGDI mutant that causes mental retardation in humans.

---

Organizational Affiliation: 

Department of Physical Biochemistry, Max-Planck-Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Secretory pathway GDP dissociation inhibitor	G	453	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: GDI1 (SEC19)
Find proteins for P39958 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: GDI1 Go to UniProtKB:  P39958

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
GTP-binding protein YPT1	Y	206	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: YPT1 (YP2)
Find proteins for P01123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P01123

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GDP	Y	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	Y	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
GER	Y	GERAN-8-YL GERAN C20 H34 HSOYJGBJQAKCNA-CAIKYXSQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.216 
• R-Value Work: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 47.503	α = 90.00
b = 119.577	β = 90.61
c = 60.723	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data scaling
CNS	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-01 
• Released Date: 2004-09-01 
• Deposition Author(s): Rak, A., Pylypenko, O., Durek, T., Watzke, A., Kushnir, S., Brunsveld, L., Waldmann, H., Goody, R.S., Alexandrov, K.

Revision History 

• Version 1.0: 2004-09-01
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance