Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.17 kDa 
• Atom Count: 3038 
• Modelled Residue Count: 370 
• Deposited Residue Count: 392 
• Unique protein chains: 2

2WWX

Crystal structure of the SidM/DrrA(GEF/GDF domain)-Rab1(GTPase domain) complex

• PDB DOI: 10.2210/pdb2WWX/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens, Legionella pneumophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-10-30 Released: 2009-12-08 
• Deposition Author(s): Suh, H.Y., Lee, D.W., Woo, J.S., Oh, B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.231 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

Literature

Structural Insights Into the Dual Nucleotide Exchange and Gdi Displacement Activity of Sidm/Drra

Suh, H.Y., Lee, D.W., Lee, K.H., Ku, B., Choi, S.J., Woo, J.S., Kim, Y.G., Oh, B.H.

(2010) EMBO J 29: 496

• PubMed: 19942850 
• DOI: 10.1038/emboj.2009.347
• Primary Citation of Related Structures:  
  2WWX


• PubMed Abstract: 
  

GDP-bound prenylated Rabs, sequestered by GDI (GDP dissociation inhibitor) in the cytosol, are delivered to destined sub-cellular compartment and subsequently activated by GEFs (guanine nucleotide exchange factors) catalysing GDP-to-GTP exchange. The dissociation of GDI from Rabs is believed to require a GDF (GDI displacement factor). Only two RabGDFs, human PRA-1 and Legionella pneumophila SidM/DrrA, have been identified so far and the molecular mechanism of GDF is elusive. Here, we present the structure of a SidM/DrrA fragment possessing dual GEF and GDF activity in complex with Rab1. SidM/DrrA reconfigures the Switch regions of the GTPase domain of Rab1, as eukaryotic GEFs do toward cognate Rabs. Structure-based mutational analyses show that the surface of SidM/DrrA, catalysing nucleotide exchange, is involved in GDI1 displacement from prenylated Rab1:GDP. In comparison with an eukaryotic GEF TRAPP I, this bacterial GEF/GDF exhibits high binding affinity for Rab1 with GDP retained at the active site, which appears as the key feature for the GDF activity of the protein.

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Organizational Affiliation: 

Department of Life Sciences and Center for Biomolecular Recognition, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAS-RELATED PROTEIN RAB-1	A	175	Homo sapiens	Mutation(s): 1  Gene Names: RAB1A, RAB1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62820 (Homo sapiens) Explore P62820  Go to UniProtKB:  P62820
PHAROS:  P62820

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DRRA	B	217	Legionella pneumophila	Mutation(s): 0  EC: 2.7.7
UniProt
Find proteins for Q5ZSQ3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSQ3  Go to UniProtKB:  Q5ZSQ3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.231 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.88	α = 90
b = 73.803	β = 90
c = 73.665	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-30 
• Released Date: 2009-12-08 
Deposition Author(s): Suh, H.Y., Lee, D.W., Woo, J.S., Oh, B.H.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Data collection, Version format compliance