3CPJ

Crystal structure of Ypt31 in complex with yeast Rab-GDI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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This is version 1.3 of the entry. See complete history


Literature

A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism.

Ignatev, A.Kravchenko, S.Rak, A.Goody, R.S.Pylypenko, O.

(2008) J Biol Chem 283: 18377-18384

  • DOI: https://doi.org/10.1074/jbc.M709718200
  • Primary Citation of Related Structures:  
    3CPH, 3CPI, 3CPJ

  • PubMed Abstract: 

    Rab GDP dissociation inhibitors (GDI)-facilitated extraction of prenylated Rab proteins from membranes plays an important role in vesicular membrane trafficking. The investigated thermodynamic properties of yeast Rab.GDI and Rab.MRS6 complexes demonstrated differences in the Rab binding properties of the closely related Rab GDI and MRS6 proteins, consistent with their functional diversity. The importance of the Rab C terminus and its prenylation for GDI/MRS6 binding was demonstrated using both biochemical and structural data. The presented structures of the apo-form yeast Rab GDI and its two complexes with unprenylated Rab proteins, together with the earlier published structures of the prenylated Ypt1.GDI, provide evidence of allosteric regulation of the GDI lipid binding site opening, which plays a key role in the proposed mechanism of GDI-mediated Rab extraction. We suggest a model for the interaction of GDI with prenylated Rab proteins that incorporates a stepwise increase in affinity as the three different partial interactions are successively formed.


  • Organizational Affiliation

    Max-Planck Institute for Molecular Physiology Dortmund Otto-Hahn-Strasse 11, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rab GDP-dissociation inhibitorA [auth G]451Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P39958 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39958 
Go to UniProtKB:  P39958
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39958
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein YPT31/YPT8223Saccharomyces cerevisiaeMutation(s): 1 
UniProt
Find proteins for P38555 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38555 
Go to UniProtKB:  P38555
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38555
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
GDI PDBBind:  3CPJ Kd: 1.89e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.94α = 90
b = 61.43β = 103.68
c = 92.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description