4YK2

Crystal Structure of the BID Domain of Bep9 from Bartonella clarridgeiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The BID Domain of Type IV Secretion Substrates Forms a Conserved Four-Helix Bundle Topped with a Hook.

Stanger, F.V.de Beer, T.A.Dranow, D.M.Schirmer, T.Phan, I.Dehio, C.

(2017) Structure 25: 203-211

  • DOI: 10.1016/j.str.2016.10.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The BID (Bep intracellular delivery) domain functions as secretion signal in a subfamily of protein substrates of bacterial type IV secretion (T4S) systems. It mediates transfer of (1) relaxases and the attached DNA during bacterial conjugation, and ...

    The BID (Bep intracellular delivery) domain functions as secretion signal in a subfamily of protein substrates of bacterial type IV secretion (T4S) systems. It mediates transfer of (1) relaxases and the attached DNA during bacterial conjugation, and (2) numerous Bartonella effector proteins (Beps) during protein transfer into host cells infected by pathogenic Bartonella species. Furthermore, BID domains of Beps have often evolved secondary effector functions within host cells. Here, we provide crystal structures for three representative BID domains and describe a novel conserved fold characterized by a compact, antiparallel four-helix bundle topped with a hook. The conserved hydrophobic core provides a rigid scaffold to a surface that, despite a few conserved exposed residues and similarities in charge distribution, displays significant variability. We propose that the genuine function of BID domains as T4S signal may primarily depend on their rigid structure, while the plasticity of their surface may facilitate adaptation to secondary effector functions.


    Organizational Affiliation

    Focal Area Infection Biology, Biozentrum University of Basel, 4056 Basel, Switzerland; Focal Area Structural Biology and Biophysics, Biozentrum University of Basel, 4056 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bartonella effector protein (Bep) substrate of VirB T4SS
A, B
147Bartonella clarridgeiae (strain CIP 104772 / 73)
Find proteins for E6YIM5 (Bartonella clarridgeiae (strain CIP 104772 / 73))
Go to UniProtKB:  E6YIM5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 76.680α = 90.00
b = 62.310β = 90.00
c = 71.040γ = 90.00
Software Package:
Software NamePurpose
MR-Rosettaphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references