4AEQ

Crystal structure of the dimeric immunity protein Cmi solved by direct methods (Arcimboldo)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.892 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of the Dimeric Colicin M Immunity

Uson, I.Patzer, S.I.Dayana Rodriguez, D.D.Braun, V.Zeth, K.

(2012) J.Struct.Biol. 178: 45

  • DOI: 10.1016/j.jsb.2012.02.004

  • PubMed Abstract: 
  • Bacteriocins are proteins secreted by many bacterial cells to kill related bacteria of the same niche. To avoid their own suicide through reuptake of secreted bacteriocins, these bacteria protect themselves by co-expression of immunity proteins in th ...

    Bacteriocins are proteins secreted by many bacterial cells to kill related bacteria of the same niche. To avoid their own suicide through reuptake of secreted bacteriocins, these bacteria protect themselves by co-expression of immunity proteins in the compartment of colicin destination. In Escherichia coli the colicin M (Cma) is inactivated by the interaction with the Cma immunity protein (Cmi). We have crystallized and solved the structure of Cmi at a resolution of 1.95Å by the recently developed ab initio phasing program ARCIMBOLDO. The monomeric structure of the mature 10kDa protein comprises a long N-terminal α-helix and a four-stranded C-terminal β-sheet. Dimerization of this fold is mediated by an extended interface of hydrogen bond interactions between the α-helix and the four-stranded β-sheet of the symmetry related molecule. Two intermolecular disulfide bridges covalently connect this dimer to further lock this complex. The Cmi protein resembles an example of a 3D domain swapping being stalled through physical linkage. The dimer is a highly charged complex with a significant surplus of negative charges presumably responsible for interactions with Cma. Dimerization of Cmi was also demonstrated to occur in vivo. Although the Cmi-Cma complex is unique among bacteria, the general fold of Cmi is representative for a class of YebF-like proteins which are known to be secreted into the external medium by some Gram-negative bacteria.


    Organizational Affiliation

    Instituto de Biología Molecular de Barcelona, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COLICIN-M IMMUNITY PROTEIN
A
98Escherichia coliMutation(s): 0 
Gene Names: cmi
Find proteins for P18002 (Escherichia coli)
Go to UniProtKB:  P18002
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.892 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 66.058α = 90.00
b = 83.552β = 90.00
c = 38.281γ = 90.00
Software Package:
Software NamePurpose
Arcimboldophasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Other
  • Version 1.2: 2012-04-18
    Type: Other