1IW7

Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution

Vassylyev, D.G.Sekine, S.Laptenko, O.Lee, J.Vassylyeva, M.N.Borukhov, S.Yokoyama, S.

(2002) NATURE 417: 712-719

  • DOI: 10.1038/nature752

  • PubMed Abstract: 
  • In bacteria, the binding of a single protein, the initiation factor sigma, to a multi-subunit RNA polymerase core enzyme results in the formation of a holoenzyme, the active form of RNA polymerase essential for transcription initiation. Here we repor ...

    In bacteria, the binding of a single protein, the initiation factor sigma, to a multi-subunit RNA polymerase core enzyme results in the formation of a holoenzyme, the active form of RNA polymerase essential for transcription initiation. Here we report the crystal structure of a bacterial RNA polymerase holoenzyme from Thermus thermophilus at 2.6 A resolution. In the structure, two amino-terminal domains of the sigma subunit form a V-shaped structure near the opening of the upstream DNA-binding channel of the active site cleft. The carboxy-terminal domain of sigma is near the outlet of the RNA-exit channel, about 57 A from the N-terminal domains. The extended linker domain forms a hairpin protruding into the active site cleft, then stretching through the RNA-exit channel to connect the N- and C-terminal domains. The holoenzyme structure provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation.


    Organizational Affiliation

    Cellular Signaling Laboratory, RIKEN Harima Institute at Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan. dmitry@yumiyoshi.harima.riken.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase alpha subunit
A, B, K, L
315Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q5SHR6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHR6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase beta subunit
C, M
1119Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q8RQE9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase beta subunit
D, N
1524Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpoC
EC: 2.7.7.6
Find proteins for Q8RQE8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase omega subunit
E, O
99Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q8RQE7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma-70 subunit
F, P
423Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: sigA
Find proteins for Q5SKW1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKW1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PB
Query on PB

Download SDF File 
Download CCD File 
D, N
LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, K, L, M, N, O, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.228 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 236.350α = 90.00
b = 236.350β = 90.00
c = 249.040γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-26
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance