3MLQ

Crystal structure of the Thermus thermophilus transcription-repair coupling factor RNA polymerase interacting domain with the Thermus aquaticus RNA polymerase beta1 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.

Westblade, L.F.Campbell, E.A.Pukhrambam, C.Padovan, J.C.Nickels, B.E.Lamour, V.Darst, S.A.

(2010) Nucleic Acids Res 38: 8357-8369

  • DOI: 10.1093/nar/gkq692
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The transcription-repair coupling factor (TRCF, the product of the mfd gene) is a widely conserved bacterial protein that mediates transcription-coupled DNA repair. TRCF uses its ATP-dependent DNA translocase activity to remove transcription complexe ...

    The transcription-repair coupling factor (TRCF, the product of the mfd gene) is a widely conserved bacterial protein that mediates transcription-coupled DNA repair. TRCF uses its ATP-dependent DNA translocase activity to remove transcription complexes stalled at sites of DNA damage, and stimulates repair by recruiting components of the nucleotide excision repair pathway to the site. A protein/protein interaction between TRCF and the β-subunit of RNA polymerase (RNAP) is essential for TRCF function. CarD (also called CdnL), an essential regulator of rRNA transcription in Mycobacterium tuberculosis, shares a homologous RNAP interacting domain with TRCF and also interacts with the RNAP β-subunit. We determined the 2.9-Å resolution X-ray crystal structure of the RNAP interacting domain of TRCF complexed with the RNAP-β1 domain, which harbors the TRCF interaction determinants. The structure reveals details of the TRCF/RNAP protein/protein interface, providing a basis for the design and interpretation of experiments probing TRCF, and by homology CarD, function and interactions with the RNAP.


    Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
A, B, C, D
188Thermus aquaticusMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q9KWU7 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU7

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcription-repair coupling factor
E, F, G, H
71Thermus thermophilus HB27Mutation(s): 0 
Gene Names: mfdTT_C0533
EC: 3.6.4
Find proteins for Q72KB4 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72KB4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.585α = 90
b = 106.585β = 90
c = 122.301γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description