Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51418.00 
• Atom Count: 3179 
• Residue Count: 444 
• Unique protein chains: 2

2OT3

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

• DOI: 10.2210/pdb2OT3/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2007-02-07 Released: 2007-04-24 
• Deposition Author(s): Delprato, A., Lambright, D.

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Experimental Data Snapshot

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

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

• PubMed: 17450153 
• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Rab5 GDP/GTP exchange factor	A	274	Homo sapiens	Mutation(s): 0  Gene Names: RABGEF1 (RABEX5)
Find proteins for Q9UJ41 (Homo sapiens) Go to Gene View: RABGEF1 Go to UniProtKB:  Q9UJ41

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ras-related protein Rab-21	B	170	Homo sapiens	Mutation(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 = 71.897	α = 90.00
b = 113.400	β = 90.00
c = 60.533	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
PHASER	phasing
HKL-2000	data collection
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-07 
• Released Date: 2007-04-24 
• Deposition Author(s): Delprato, A., Lambright, D.

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