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 

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

  • 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 reg ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Secretory pathway GDP dissociation inhibitor
G
453Saccharomyces 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
MoleculeChainsSequence LengthOrganismDetails
GTP-binding protein YPT1
Y
206Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: YPT1 (YP2)
Find proteins for P01123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P01123
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

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Download CCD File 
Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GER
Query on GER

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

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Download CCD File 
Y
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 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 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.660α = 90.00
b = 120.230β = 90.67
c = 60.550γ = 90.00
Software Package:
Software NamePurpose
ProDCdata collection
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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