2OT3

Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for Rab GTPase activation by VPS9 domain exchange factors.

Delprato, A.Lambright, D.G.

(2007) Nat.Struct.Mol.Biol. 14: 406-412

  • DOI: 10.1038/nsmb1232

  • PubMed Abstract: 
  • RABEX-5 and other exchange factors with VPS9 domains regulate endocytic trafficking through activation of the Rab family GTPases RAB5, RAB21 and RAB22. Here we report the crystal structure of the RABEX-5 catalytic core in complex with nucleotide-free ...

    RABEX-5 and other exchange factors with VPS9 domains regulate endocytic trafficking through activation of the Rab family GTPases RAB5, RAB21 and RAB22. Here we report the crystal structure of the RABEX-5 catalytic core in complex with nucleotide-free RAB21, a key intermediate in the exchange reaction pathway. The structure reveals how VPS9 domain exchange factors recognize Rab GTPase substrates, accelerate GDP release and stabilize the nucleotide-free conformation. We further identify an autoinhibitory element in a predicted amphipathic helix located near the C terminus of the VPS9 domain. The autoinhibitory element overlaps with the binding site for the multivalent effector RABAPTIN-5 and potently suppresses the exchange activity of RABEX-5. Autoinhibition can be partially reversed by mutation of conserved residues on the nonpolar face of the predicted amphipathic helix or by assembly of the complex with RABAPTIN-5.


    Organizational Affiliation

    Program in Molecular Medicine and Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Two Biotech, 373 Plantation Street, Worcester, Massachusetts 01605, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rab5 GDP/GTP exchange factor
A
274Homo sapiensMutation(s): 0 
Gene Names: RABGEF1 (RABEX5)
Find proteins for Q9UJ41 (Homo sapiens)
Go to Gene View: RABGEF1
Go to UniProtKB:  Q9UJ41
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-21
B
170Homo sapiensMutation(s): 0 
Gene Names: RAB21 (KIAA0118)
Find proteins for Q9UL25 (Homo sapiens)
Go to Gene View: RAB21
Go to UniProtKB:  Q9UL25
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.897α = 90.00
b = 113.400β = 90.00
c = 60.533γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
PHASERphasing
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-24
    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: 2017-10-11
    Type: Advisory, Data collection