2BCG

Structure of doubly prenylated Ypt1:GDI complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-mediated Rab recycling

Pylypenko, O.Rak, A.Durek, T.Kushnir, S.Dursina, B.E.Thomae, N.H.Constantinescu, A.T.Brunsveld, L.Watzke, A.Waldmann, H.Goody, R.S.Alexandrov, K.

(2006) EMBO J 25: 13-23

  • DOI: 10.1038/sj.emboj.7600921
  • Primary Citation of Related Structures:  
    2BCG

  • PubMed Abstract: 
  • In eukaryotic cells Rab/Ypt GTPases represent a family of key membrane traffic controllers that associate with their targeted membranes via C-terminally conjugated geranylgeranyl groups. GDP dissociation inhibitor (GDI) is a general and essential regulat ...

    In eukaryotic cells Rab/Ypt GTPases represent a family of key membrane traffic controllers that associate with their targeted membranes via C-terminally conjugated geranylgeranyl groups. GDP dissociation inhibitor (GDI) is a general and essential regulator of Rab recycling that extracts prenylated Rab proteins from membranes at the end of their cycle of activity and facilitates their delivery to the donor membranes. Here, we present the structure of a complex between GDI and a doubly prenylated Rab protein. We show that one geranylgeranyl residue is deeply buried in a hydrophobic pocket formed by domain II of GDI, whereas the other lipid is more exposed to solvent and is skewed across several atoms of the first moiety. Based on structural information and biophysical measurements, we propose mechanistic and thermodynamic models for GDI and Rab escort protein-mediated interaction of RabGTPase with intracellular membranes.


    Organizational Affiliation

    Max-Planck-Institute for Molecular Physiology, Dortmund, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Secretory pathway GDP dissociation inhibitor G453Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GDI1
Find proteins for P39958 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39958 
Go to UniProtKB:  P39958
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding protein YPT1 Y206Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: YPT1
Find proteins for P01123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P01123 
Go to UniProtKB:  P01123
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
Y
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GER
Query on GER

Download Ideal Coordinates CCD File 
G
GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
Y
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.66α = 90
b = 120.23β = 90.67
c = 60.55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ProDCdata collection
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description