1L9U

THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution.

Murakami, K.S.Masuda, S.Darst, S.A.

(2002) Science 296: 1280-1284

  • DOI: 10.1126/science.1069594

  • PubMed Abstract: 
  • The crystal structure of the initiating form of Thermus aquaticus RNA polymerase, containing core RNA polymerase (alpha2betabeta'omega) and the promoter specificity sigma subunit, has been determined at 4 angstrom resolution. Important structural fea ...

    The crystal structure of the initiating form of Thermus aquaticus RNA polymerase, containing core RNA polymerase (alpha2betabeta'omega) and the promoter specificity sigma subunit, has been determined at 4 angstrom resolution. Important structural features of the RNA polymerase and their roles in positioning sigma within the initiation complex are delineated, as well as the role played by sigma in modulating the opening of the RNA polymerase active-site channel. The two carboxyl-terminal domains of sigma are separated by 45 angstroms on the surface of the RNA polymerase, but are linked by an extended loop. The loop winds near the RNA polymerase active site, where it may play a role in initiating nucleotide substrate binding, and out through the RNA exit channel. The advancing RNA transcript must displace the loop, leading to abortive initiation and ultimately to sigma release.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA POLYMERASE, ALPHA SUBUNIT
A, B, J, K
314Thermus aquaticusGene Names: rpoA
EC: 2.7.7.6
Find proteins for Q9KWU8 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA POLYMERASE, BETA SUBUNIT
C, L
1118Thermus aquaticusGene Names: rpoB
EC: 2.7.7.6
Find proteins for Q9KWU7 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA POLYMERASE, BETA-PRIME SUBUNIT
D, M
1524Thermus aquaticusGene Names: rpoC
EC: 2.7.7.6
Find proteins for Q9KWU6 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA POLYMERASE, OMEGA SUBUNIT
E, N
99Thermus aquaticusGene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q9EVV4 (Thermus aquaticus)
Go to UniProtKB:  Q9EVV4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
SIGMA FACTOR SIGA
H, Q
332Thermus aquaticusGene Names: sigA
Find proteins for Q9EZJ8 (Thermus aquaticus)
Go to UniProtKB:  Q9EZJ8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 155.000α = 90.00
b = 271.200β = 91.40
c = 155.300γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MLPHAREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-22
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance