RNA Polymerase interacting protein YkzG from Geobacillus stearothermophilus

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


epsilon, a New Subunit of RNA Polymerase Found in Gram-Positive Bacteria

Keller, A.N.Yang, X.Wiedermannova, J.Delumeau, O.Krasny, L.Lewis, P.J.

(2014) J Bacteriol 196: 3622-3632

  • DOI: https://doi.org/10.1128/JB.02020-14
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    RNA polymerase in bacteria is a multisubunit protein complex that is essential for gene expression. We have identified a new subunit of RNA polymerase present in the high-A+T Firmicutes phylum of Gram-positive bacteria and have named it ε. Previously ε had been identified as a small protein (ω1) that copurified with RNA polymerase. We have solved the structure of ε by X-ray crystallography and show that it is not an ω subunit. Rather, ε bears remarkable similarity to the Gp2 family of phage proteins involved in the inhibition of host cell transcription following infection. Deletion of ε shows no phenotype and has no effect on the transcriptional profile of the cell. Determination of the location of ε within the assembly of RNA polymerase core by single-particle analysis suggests that it binds toward the downstream side of the DNA binding cleft. Due to the structural similarity of ε with Gp2 and the fact they bind similar regions of RNA polymerase, we hypothesize that ε may serve a role in protection from phage infection.

  • Organizational Affiliation

    Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geobacillus stearothermophilus YkzG
A, B, C, D, E
A, B, C, D, E, F, G, H
65Geobacillus stearothermophilusMutation(s): 0 
Find proteins for A0A0K2H5X8 (Geobacillus stearothermophilus (strain DSM 13240 / CIP 106956 / 10))
Explore A0A0K2H5X8 
Go to UniProtKB:  A0A0K2H5X8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K2H5X8
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.65α = 90
b = 82.78β = 92.76
c = 83.43γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
BUCCANEERmodel building
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references