3GQM | pdb_00003gqm

Crystal structure of Cell Inhibiting Factor (Cif) from Burkholderia pseudomallei (CifBp)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.259 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3GQM

This is version 1.2 of the entry. See complete history

Literature

Crystal structures of Cif from bacterial pathogens Photorhabdus luminescens and Burkholderia pseudomallei.

Crow, A.Race, P.R.Jubelin, G.Varela Chavez, C.Escoubas, J.M.Oswald, E.Banfield, M.J.

(2009) PLoS One 4: e5582-e5582

  • DOI: https://doi.org/10.1371/journal.pone.0005582
  • Primary Citation Related Structures: 
    3GQJ, 3GQM

  • PubMed Abstract: 

    A pre-requisite for bacterial pathogenesis is the successful interaction of a pathogen with a host. One mechanism used by a broad range of Gram negative bacterial pathogens is to deliver effector proteins directly into host cells through a dedicated type III secretion system where they modulate host cell function. The cycle inhibiting factor (Cif) family of effector proteins, identified in a growing number of pathogens that harbour functional type III secretion systems and have a wide host range, arrest the eukaryotic cell cycle. Here, the crystal structures of Cifs from the insect pathogen/nematode symbiont Photorhabdus luminescens (a gamma-proteobacterium) and human pathogen Burkholderia pseudomallei (a beta-proteobacterium) are presented. Both of these proteins adopt an overall fold similar to the papain sub-family of cysteine proteases, as originally identified in the structure of a truncated form of Cif from Enteropathogenic E. coli (EPEC), despite sharing only limited sequence identity. The structure of an N-terminal region, referred to here as the 'tail-domain' (absent in the EPEC Cif structure), suggests a surface likely to be involved in host-cell substrate recognition. The conformation of the Cys-His-Gln catalytic triad is retained, and the essential cysteine is exposed to solvent and addressable by small molecule reagents. These structures and biochemical work contribute to the rapidly expanding literature on Cifs, and direct further studies to better understand the molecular details of the activity of these proteins.


  • Organizational Affiliation
    • Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 61.71 kDa 
  • Atom Count: 4,017 
  • Modeled Residue Count: 494 
  • Deposited Residue Count: 552 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell Inhibiting Factor (CifBp)
A, B
276Burkholderia pseudomalleiMutation(s): 0 
Gene Names: BPSS1385
EC: 3.5.1.44
UniProt
Find proteins for Q63KH5 (Burkholderia pseudomallei (strain K96243))
Explore Q63KH5 
Go to UniProtKB:  Q63KH5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63KH5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.259 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.893α = 90
b = 77.744β = 90
c = 115.016γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Refinement description