2CW0

Crystal structure of Thermus thermophilus RNA polymerase holoenzyme at 3.3 angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.282 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation

Tuske, S.Sarafianos, S.G.Wang, X.Hudson, B.Sineva, E.Mukhopadhyay, J.Birktoft, J.J.Leroy, O.Ismail, S.Clark Jr., A.D.Dharia, C.Napoli, A.Laptenko, O.Lee, J.Borukhov, S.Ebright, R.H.Arnold, E.

(2005) Cell 122: 541-552

  • DOI: https://doi.org/10.1016/j.cell.2005.07.017
  • Primary Citation of Related Structures:  
    1ZYR, 2CW0

  • PubMed Abstract: 

    We define the target, mechanism, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the tetramic acid antibiotic streptolydigin (Stl). Stl binds to a site adjacent to but not overlapping the RNAP active center and stabilizes an RNAP-active-center conformational state with a straight-bridge helix. The results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations exist and that cycling between straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations is required for RNAP function. The results set bounds on models for RNAP function and suggest strategies for design of novel antibacterial agents.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase alpha chainA,
B,
G [auth K],
H [auth L]
315Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SHR6
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta chainC,
I [auth M]
1,119Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta' chainD,
J [auth N]
1,524Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase omega chainE,
K [auth O]
99Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor rpoDF,
L [auth P]
423Thermus thermophilus HB27Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.282 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 236.15α = 90
b = 236.15β = 90
c = 249.88γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2012-09-05
    Changes: Refinement description
  • Version 1.4: 2019-12-04
    Changes: Derived calculations
  • Version 1.5: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description