1G17

CRYSTAL STRUCTURE OF SEC4-GUANOSINE-5'-(BETA,GAMMA)-IMIDOTRIPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of a Rab protein in its inactive and active conformations.

Stroupe, C.Brunger, A.T.

(2000) J.Mol.Biol. 304: 585-598

  • DOI: 10.1006/jmbi.2000.4236
  • Primary Citation of Related Structures:  1G16

  • PubMed Abstract: 
  • We have determined crystal structures of Sec4, a member of the Rab family in the G protein superfamily, in two states: bound to GDP, and to a non-hydrolyzable GTP analog, guanosine-5'-(beta, gamma)-imidotriphosphate (GppNHp). This represents the firs ...

    We have determined crystal structures of Sec4, a member of the Rab family in the G protein superfamily, in two states: bound to GDP, and to a non-hydrolyzable GTP analog, guanosine-5'-(beta, gamma)-imidotriphosphate (GppNHp). This represents the first structure of a Rab protein bound to GDP. Sec4 in both states grossly resembles other G proteins bound to GDP and GppNHp. In Sec4-GppNHp, structural features common to active Rab proteins are observed. In Sec4-GDP, the switch I region is highly disordered and displaced relative to the switch I region of Ras-GDP. In two of the four molecules of Sec4-GDP in the asymmetric unit of the Sec4-GDP crystals, the switch II region adopts a conformation similar to that seen in the structure of the small G protein Ran bound to GDP. This allows residues threonine 76, glutamate 80, and arginine 81 of Sec4 to make contacts with other conserved residues and water molecules important for nucleotide binding. In the other two molecules in the asymmetric unit, these interactions do not take place. This structural variability in both the switch I and switch II regions of GDP-bound Sec4 provides a possible explanation for the high off-rate of GDP bound to Sec4, and suggests a mechanism for regulation of the GTPase cycle of Rab proteins by GDI proteins.


    Organizational Affiliation

    The Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305-548, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAS-RELATED PROTEIN SEC4
A, B
170Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SEC4 (SRO6)
Find proteins for P07560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07560
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.264 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 84.504α = 90.00
b = 84.504β = 90.00
c = 86.469γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance