3N6O

Crystal structure of the GEF and P4M domain of DrrA/SidM from Legionella pneumophila

• PDB DOI: https://doi.org/10.2210/pdb3N6O/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2010-05-26 Released: 2010-07-28 
• Deposition Author(s): Schoebel, S., Blankenfeldt, W., Goody, R.S., Itzen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.236 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Literature

High-affinity binding of phosphatidylinositol 4-phosphate by Legionella pneumophila DrrA.

Schoebel, S., Blankenfeldt, W., Goody, R.S., Itzen, A.

(2010) EMBO Rep 11: 598-604

• PubMed: 20616805 
• DOI: https://doi.org/10.1038/embor.2010.97
• Primary Citation of Related Structures:  
  3N6O


• PubMed Abstract: 
  

  The DrrA protein of Legionella pneumophila is involved in mistargeting of endoplasmic reticulum-derived vesicles to Legionella-containing vacuoles through recruitment of the small GTPase Rab1. To this effect, DrrA binds specifically to phosphatidylinositol 4-phosphate (PtdIns(4)P) lipids on the cytosolic surface of the phagosomal membrane shortly after infection. In this study, we present the atomic structure of the PtdIns(4)P-binding domain of a protein (DrrA) from a human pathogen. A detailed kinetic investigation of its interaction with PtdIns(4)P reveals that DrrA binds to this phospholipid with, as yet unprecedented, high affinity, suggesting that DrrA can sense a very low abundance of the lipid.

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Organizational Affiliation: 

Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, North Rhine-Westphalia, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 71.02 kDa 
• Atom Count: 4,966 
• Modelled Residue Count: 604 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
guanine nucleotide exchange factor	A, B	311	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: DrrA, lpg2464 Membrane Entity: Yes
UniProt
Find proteins for Q5ZSQ3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSQ3  Go to UniProtKB:  Q5ZSQ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.236 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.962	α = 90
b = 75.375	β = 90
c = 130.965	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Schoebel, S., Blankenfeldt, W., Goody, R.S., Itzen, A.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations