2OCY

Complex of the guanine exchange factor Sec2p and the Rab GTPase Sec4p


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Catalytic Coiled Coil: Structural Insights into the Activation of the Rab GTPase Sec4p by Sec2p.

Dong, G.Medkova, M.Novick, P.Reinisch, K.M.

(2007) Mol.Cell 25: 455-462

  • DOI: 10.1016/j.molcel.2007.01.013

  • PubMed Abstract: 
  • Rab GTPases, the largest subgroup in the superfamily of Ras-like GTPases, play regulatory roles in multiple steps of intracellular vesicle trafficking. They are activated by guanine nucleotide exchange factors (GEFs), which catalyze the interconversi ...

    Rab GTPases, the largest subgroup in the superfamily of Ras-like GTPases, play regulatory roles in multiple steps of intracellular vesicle trafficking. They are activated by guanine nucleotide exchange factors (GEFs), which catalyze the interconversion of the GDP-bound, or inactive, form of Rab to the GTP-bound, or active, form. Relatively little is known of the mechanisms by which GEFs activate Rabs. Here, we present the crystal structure of the GEF domain of Sec2p in complex with its Rab partner Sec4p. The Sec2p GEF domain is a 220 Angstroms long coiled coil, striking in its simplicity and in the use of the coiled-coil motif for catalysis. The structure suggests a mechanism whereby Sec2p induces extensive structural rearrangements in the Sec4p switch regions and phosphate-binding loop that are incompatible with nucleotide binding. We show that Sec2p is specific for Sec4p and that specificity determinants reside in the two switch regions of Sec4p.


    Organizational Affiliation

    Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rab guanine nucleotide exchange factor SEC2
A, B
154Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SEC2
Find proteins for P17065 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17065
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein SEC4
C
170Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SEC4 (SRO6)
Find proteins for P07560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07560
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.250 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.999α = 90.00
b = 92.999β = 90.00
c = 295.909γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
SHARPphasing
HKL-2000data reduction
CNSrefinement
SHELXSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-27
    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: Advisory, Refinement description