4GZY

Crystal structures of bacterial RNA Polymerase paused elongation complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.266 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of transcriptional pausing in bacteria.

Weixlbaumer, A.Leon, K.Landick, R.Darst, S.A.

(2013) Cell 152: 431-441

  • DOI: https://doi.org/10.1016/j.cell.2012.12.020
  • Primary Citation of Related Structures:  
    4GZY, 4GZZ

  • PubMed Abstract: 

    Transcriptional pausing by multisubunit RNA polymerases (RNAPs) is a key mechanism for regulating gene expression in both prokaryotes and eukaryotes and is a prerequisite for transcription termination. Pausing and termination states are thought to arise through a common, elemental pause state that is inhibitory for nucleotide addition. We report three crystal structures of Thermus RNAP elemental paused elongation complexes (ePECs). The structures reveal the same relaxed, open-clamp RNAP conformation in the ePEC that may arise by failure to re-establish DNA contacts during translocation. A kinked bridge-helix sterically blocks the RNAP active site, explaining how this conformation inhibits RNAP catalytic activity. Our results provide a framework for understanding how RNA hairpin formation stabilizes the paused state and how the ePEC intermediate facilitates termination.


  • Organizational Affiliation

    The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
315Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoATTHA1664
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 subunit beta1,119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoBTTHA1813
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,534Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoCTTHA1812
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoZTTHA1561
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q8RQE7 
Go to UniProtKB:  Q8RQE7
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UniProt GroupQ8RQE7
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
non-template DNAF [auth N]13synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA transcriptG [auth R]29synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
template DNAH [auth T]22synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.266 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.21α = 90
b = 207.21β = 90
c = 203.223γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description