3JZA | pdb_00003jza

Crystal structure of human Rab1b in complex with the GEF domain of DrrA/SidM from Legionella pneumophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.234 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3JZA

This is version 1.3 of the entry. See complete history

Literature

RabGDI displacement by DrrA from Legionella is a consequence of its guanine nucleotide exchange activity.

Schoebel, S.Oesterlin, L.K.Blankenfeldt, W.Goody, R.S.Itzen, A.

(2009) Mol Cell 36: 1060-1072

  • DOI: https://doi.org/10.1016/j.molcel.2009.11.014
  • Primary Citation Related Structures: 
    3JZ9, 3JZA

  • PubMed Abstract: 

    Prenylated Rab proteins exist in the cytosol as soluble, high-affinity complexes with GDI that need to be disrupted for membrane attachment and targeting of Rab proteins. The Legionella pneumophila protein DrrA displaces GDI from Rab1:GDI complexes, incorporating Rab1 into Legionella-containing vacuoles and activating Rab1 by exchanging GDP for GTP. Here, we present the crystal structure of a complex between the GEF domain of DrrA and Rab1 and a detailed kinetic analysis of this exchange. DrrA efficiently catalyzes nucleotide exchange and mimics the general nucleotide exchange mechanism of mammalian GEFs for Ras-like GTPases. We show that the GEF activity of DrrA is sufficient to displace prenylated Rab1 from the Rab1:GDI complex. Thus, apparent GDI displacement by DrrA is linked directly to nucleotide exchange, suggesting a basic model for GDI displacement and specificity of Rab localization that does not require discrete GDI displacement activity.


  • Organizational Affiliation
    • Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, NRW, Germany.

Macromolecule Content 

  • Total Structure Weight: 41.86 kDa 
  • Atom Count: 3,101 
  • Modeled Residue Count: 361 
  • Deposited Residue Count: 372 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras-related protein Rab-1B175Homo sapiensMutation(s): 0 
Gene Names: RAB1B
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0U4 (Homo sapiens)
Explore Q9H0U4 
Go to UniProtKB:  Q9H0U4
PHAROS:  Q9H0U4
GTEx:  ENSG00000174903 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0U4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein DrrA197Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: lpg2464
EC: 2.7.7.108
UniProt
Find proteins for Q5ZSQ3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZSQ3 
Go to UniProtKB:  Q5ZSQ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZSQ3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.234 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.756α = 90
b = 100.756β = 90
c = 146.36γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations