1L9Z

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.50 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
  • Primary Citation of Related Structures:  
    1L9Z

  • 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-angstrom resolution map ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RNA POLYMERASE, ALPHA SUBUNITC [auth A],
D [auth B]		314Thermus aquaticusMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU8 (Thermus aquaticus)
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UniProt GroupQ9KWU8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA POLYMERASE, BETA SUBUNITE [auth C]1,118Thermus aquaticusMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU7 (Thermus aquaticus)
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UniProt GroupQ9KWU7
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA POLYMERASE, BETA-PRIME SUBUNITF [auth D]1,524Thermus aquaticusMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU6 (Thermus aquaticus)
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UniProt GroupQ9KWU6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA POLYMERASE, OMEGA SUBUNITG [auth E]99Thermus aquaticusMutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
UniProt
Find proteins for Q9EVV4 (Thermus aquaticus)
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UniProt GroupQ9EVV4
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
SIGMA FACTOR SIGAH438Thermus aquaticusMutation(s): 0 
Gene Names: rpoD, sigA
UniProt
Find proteins for Q9EZJ8 (Thermus aquaticus)
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UniProt GroupQ9EZJ8
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Entity ID: 1
MoleculeChainsLengthOrganismImage
nontemplate DNA strandA [auth U]35N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
template DNA strandB [auth T]30N/A
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
J [auth D],
K [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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I [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.50 Å
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.947α = 90
b = 180.947β = 90
c = 523.461γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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