3RWO

Crystal structure of YPT32 in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The activation cycle of Rab GTPase Ypt32 reveals structural determinants of effector recruitment and GDI binding.

Sultana, A.Jin, Y.Dregger, C.Franklin, E.Weisman, L.S.Khan, A.R.

(2011) FEBS Lett 585: 3520-3527

  • DOI: 10.1016/j.febslet.2011.10.013
  • Primary Citation of Related Structures:  
    3RWM, 3RWO

  • PubMed Abstract: 
  • Rab GTPases localize to distinct sub-cellular compartments and regulate vesicle trafficking in eukaryotic cells. Yeast Rabs Ypt31/32 and Sec4 have 68% homology and bind to common interactors, yet play distinct roles in the transport of exocytic vesicles. The structures of Ypt31/32 have not previously been reported in the uncomplexed state ...

    Rab GTPases localize to distinct sub-cellular compartments and regulate vesicle trafficking in eukaryotic cells. Yeast Rabs Ypt31/32 and Sec4 have 68% homology and bind to common interactors, yet play distinct roles in the transport of exocytic vesicles. The structures of Ypt31/32 have not previously been reported in the uncomplexed state. We describe the crystal structures of GTP and GDP forms of Ypt32 to understand the molecular basis for Rab function. The structure of Ypt32(GTP) reveals that the switch II conformation is distinct from Sec4(GTP) in spite of a highly conserved amino acid sequence. Also, Ypt32(GDP) reveals a remarkable change in conformation of the switch II helix induced by binding to GDI, which has not been described previously.


    Organizational Affiliation

    School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding protein YPT32/YPT11B [auth A],
A [auth B]
185Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: YGL210WYPT11YPT32
UniProt
Find proteins for P51996 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P51996 
Go to UniProtKB:  P51996
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51996
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
C [auth B],
E [auth A]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth B],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130α = 90
b = 45.2β = 110.5
c = 73.4γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2011-11-09
    Changes: Database references
  • Version 1.2: 2011-12-14
    Changes: Database references