1L9U

THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1126/science.1069594
  • Primary Citation of Related Structures:  
    1L9U

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA POLYMERASE, ALPHA SUBUNITA,
B,
G [auth J],
H [auth K]
314Thermus aquaticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU8 (Thermus aquaticus)
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UniProt GroupQ9KWU8
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA POLYMERASE, BETA SUBUNITC,
I [auth L]
1,118Thermus aquaticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU7 (Thermus aquaticus)
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UniProt GroupQ9KWU7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RNA POLYMERASE, BETA-PRIME SUBUNITD,
J [auth M]
1,524Thermus aquaticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU6 (Thermus aquaticus)
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UniProt GroupQ9KWU6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA POLYMERASE, OMEGA SUBUNITE,
K [auth N]
99Thermus aquaticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9EVV4 (Thermus aquaticus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
SIGMA FACTOR SIGAF [auth H],
L [auth Q]
332Thermus aquaticusMutation(s): 0 
Gene Names: RPOD
UniProt
Find proteins for Q9EZJ8 (Thermus aquaticus)
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UniProt GroupQ9EZJ8
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155α = 90
b = 271.2β = 91.4
c = 155.3γ = 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: 2002-05-22
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations