4I1O

Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of Rab1b deactivation by the Legionella pneumophila GAP LepB.

Mihai Gazdag, E.Streller, A.Haneburger, I.Hilbi, H.Vetter, I.R.Goody, R.S.Itzen, A.

(2013) Embo Rep. 14: 199-205

  • DOI: 10.1038/embor.2012.211
  • Primary Citation of Related Structures:  4I1M

  • PubMed Abstract: 
  • Legionella pneumophila is an intracellularly surviving pathogen that releases about 270 different proteins into the host cell during infection. A set of secreted proteins takes control of the vesicular trafficking regulator Rab1. Legionella LepB inac ...

    Legionella pneumophila is an intracellularly surviving pathogen that releases about 270 different proteins into the host cell during infection. A set of secreted proteins takes control of the vesicular trafficking regulator Rab1. Legionella LepB inactivates Rab1 by acting as a GTPase-activating protein (GAP). We present the crystal structure of the Rab1b:LepB complex together with a thorough biochemical analysis and show that the GAP domain of LepB consists of an unusual fold. LepB acts by an atypical RabGAP mechanism that is reminiscent of classical GAPs and therefore sets the protein apart from mammalian TBC-like GAPs. Surprisingly, LepB can function as a GAP for Rab3, Rab8, Rab13 and Rab35, too, suggesting that it has a broader cellular role than previously thought.


    Organizational Affiliation

    Max-Planck-Institute of Molecular Physiology, Department of Physical Biochemistry, Dortmund 44227, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-1B
A, C, E, G
181Homo sapiensGene Names: RAB1B
Find proteins for Q9H0U4 (Homo sapiens)
Go to Gene View: RAB1B
Go to UniProtKB:  Q9H0U4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LepB
B, D, F, H
302Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)Gene Names: lepB
Find proteins for Q5ZSM7 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Go to UniProtKB:  Q5ZSM7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, C, E, G
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, E, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, C, D, G
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A, C, E, G
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 124.410α = 90.00
b = 124.410β = 90.00
c = 147.470γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Database references