1L9Z

Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex.

Murakami, K.S.Masuda, S.Campbell, E.A.Muzzin, O.Darst, S.A.

(2002) Science 296: 1285-1290

  • DOI: 10.1126/science.1069595

  • PubMed Abstract: 
  • The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (alpha2betabeta'omegasigmaA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5 ...

    The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (alpha2betabeta'omegasigmaA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map. The DNA lies across one face of the holoenzyme, completely outside the RNA polymerase active site channel. All sequence-specific contacts with core promoter elements are mediated by the sigma subunit. A universally conserved tryptophan is ideally positioned to stack on the exposed face of the base pair at the upstream edge of the transcription bubble. Universally conserved basic residues of the sigma subunit provide critical contacts with the DNA phosphate backbone and play a role in directing the melted DNA template strand into the RNA polymerase active site. The structure explains how holoenzyme recognizes promoters containing variably spaced -10 and -35 elements and provides the basis for models of the closed and open promoter complexes.


    Organizational Affiliation

    The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA POLYMERASE, ALPHA SUBUNIT
A, B
314Thermus aquaticusGene Names: rpoA
EC: 2.7.7.6
Find proteins for Q9KWU8 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA POLYMERASE, BETA SUBUNIT
C
1118Thermus aquaticusGene Names: rpoB
EC: 2.7.7.6
Find proteins for Q9KWU7 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA POLYMERASE, BETA-PRIME SUBUNIT
D
1524Thermus aquaticusGene Names: rpoC
EC: 2.7.7.6
Find proteins for Q9KWU6 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RNA POLYMERASE, OMEGA SUBUNIT
E
99Thermus aquaticusGene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q9EVV4 (Thermus aquaticus)
Go to UniProtKB:  Q9EVV4
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
SIGMA FACTOR SIGA
H
438Thermus aquaticusGene Names: sigA
Find proteins for Q9EZJ8 (Thermus aquaticus)
Go to UniProtKB:  Q9EZJ8
Entity ID: 1
MoleculeChainsLengthOrganism
nontemplate DNA strandU35N/A
Entity ID: 2
MoleculeChainsLengthOrganism
template DNA strandT30N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.5 Å
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 180.947α = 90.00
b = 180.947β = 90.00
c = 523.461γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-31
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance