4I1O

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

• PDB DOI: https://doi.org/10.2210/pdb4I1O/pdb

• Classification: PROTEIN TRANSPORT/HYDROLASE
• Organism(s): Homo sapiens, Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-11-21 Released: 2013-01-16 
• Deposition Author(s): Gazdag, E.M., Streller, A., Vetter, I.R., Goody, R.S., Itzen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

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

• PubMed: 23288104 
• DOI: https://doi.org/10.1038/embor.2012.211
• Primary Citation of Related Structures:  
  4I1M, 4I1O


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 221.23 kDa 
• Atom Count: 14,310 
• Modelled Residue Count: 1,831 
• Deposited Residue Count: 1,932 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-1B	A, C, E, G	181	Homo sapiens	Mutation(s): 0  Gene Names: RAB1B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0U4 (Homo sapiens) Explore Q9H0U4  Go to UniProtKB:  Q9H0U4
PHAROS:  Q9H0U4 GTEx:  ENSG00000174903

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LepB	B, D, F, H	302	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 3  Gene Names: lepB, lpg2490
UniProt
Find proteins for Q5ZSM7 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSM7  Go to UniProtKB:  Q5ZSM7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	J [auth A], N [auth C], U [auth E], X [auth G]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
PEG	L [auth A], P [auth C], Q [auth C], R [auth C], S [auth D], Z [auth G]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
BEF	K [auth A], O [auth C], V [auth E], Y [auth G]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG	I [auth A], M [auth C], T [auth E], W [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.41	α = 90
b = 124.41	β = 90
c = 147.47	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Gazdag, E.M., Streller, A., Vetter, I.R., Goody, R.S., Itzen, A.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2013-02-20
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description