5COG

Crystal structure of Yeast IRC4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of the DfsB Protein Family Suggest a Cationic, Helical Sibling Lethal Factor Peptide.

Taylor, J.D.Taylor, G.Hare, S.A.Matthews, S.J.

(2016) J Mol Biol 428: 554-560

  • DOI: https://doi.org/10.1016/j.jmb.2016.01.013
  • Primary Citation of Related Structures:  
    5CIV, 5COF, 5COG, 5COM, 5CQV

  • PubMed Abstract: 

    Bacteria have developed a variety of mechanisms for surviving harsh environmental conditions, nutrient stress and overpopulation. Paenibacillus dendritiformis produces a lethal protein (Slf) that is able to induce cell death in neighbouring colonies and a phenotypic switch in more distant ones. Slf is derived from the secreted precursor protein, DfsB, after proteolytic processing. Here, we present new crystal structures of DfsB homologues from a variety of bacterial species and a surprising version present in the yeast Saccharomyces cerevisiae. Adopting a four-helix bundle decorated with a further three short helices within intervening loops, DfsB belongs to a non-enzymatic class of the DinB fold. The structure suggests that the biologically active Slf fragment may possess a C-terminal helix rich in basic and aromatic residues that suggest a functional mechanism akin to that for cationic antimicrobial peptides.


  • Organizational Affiliation

    Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IRC4
A, B
191Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: IRC4YDR540C
UniProt
Find proteins for Q03036 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03036 
Go to UniProtKB:  Q03036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03036
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.57α = 90
b = 38.69β = 108.59
c = 67.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
xia2data scaling
xia2data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description