1UKV | pdb_00001ukv

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

• PDB DOI: https://doi.org/10.2210/pdb1UKV/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.216 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

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: https://doi.org/10.1126/science.1087761
• Primary Citation of Related Structures:  
  1UKV


• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 75.45 kDa 
• Atom Count: 6,126 
• Modeled Residue Count: 639 
• Deposited Residue Count: 659 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Secretory pathway GDP dissociation inhibitor	A [auth G]	453	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P39958 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39958  Go to UniProtKB:  P39958

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein YPT1	B [auth Y]	206	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P01123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P01123  Go to UniProtKB:  P01123

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.216 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.503	α = 90
b = 119.577	β = 90.61
c = 60.723	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Structure summary