5COG | pdb_00005cog

Crystal structure of Yeast IRC4

• PDB DOI: https://doi.org/10.2210/pdb5COG/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-20 Released: 2016-02-03 
• Deposition Author(s): Taylor, J.D., Matthews, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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 Biology 428: 554-560

• PubMed: 26804569 
• DOI: https://doi.org/10.1016/j.jmb.2016.01.013
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom. Electronic address: [e-mail].

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: 46.22 kDa 
• Atom Count: 3,527 
• Modeled Residue Count: 337 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IRC4	A, B	191	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: IRC4, YDR540C
UniProt
Find proteins for Q03036 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03036  Go to UniProtKB:  Q03036

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	E [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.57	α = 90
b = 38.69	β = 108.59
c = 67.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
xia2	data scaling
xia2	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Taylor, J.D., Matthews, S.J.

Revision History  

• 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