5EZK

RNA polymerase model placed by Molecular replacement into X-ray diffraction map of DNA-bound RNA Polymerase-Sigma 54 holoenzyme complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.50 Å
  • R-Value Free: 0.470 
  • R-Value Work: 0.470 
  • R-Value Observed: 0.470 

wwPDB Validation   3D Report Full Report


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Literature

TRANSCRIPTION. Structures of the RNA polymerase- Sigma 54 reveal new and conserved regulatory strategies.

Yang, Y.Darbari, V.C.Zhang, N.Lu, D.Glyde, R.Wang, Y.P.Winkelman, J.T.Gourse, R.L.Murakami, K.S.Buck, M.Zhang, X.

(2015) Science 349: 882-885

  • DOI: 10.1126/science.aab1478
  • Primary Citation of Related Structures:  
    5BYH, 5NWT, 5EZK

  • PubMed Abstract: 
  • Transcription by RNA polymerase (RNAP) in bacteria requires specific promoter recognition by σ factors. The major variant σ factor (σ(54)) initially forms a transcriptionally silent complex requiring specialized adenosine triphosphate-dependent activ ...

    Transcription by RNA polymerase (RNAP) in bacteria requires specific promoter recognition by σ factors. The major variant σ factor (σ(54)) initially forms a transcriptionally silent complex requiring specialized adenosine triphosphate-dependent activators for initiation. Our crystal structure of the 450-kilodalton RNAP-σ(54) holoenzyme at 3.8 angstroms reveals molecular details of σ(54) and its interactions with RNAP. The structure explains how σ(54) targets different regions in RNAP to exert its inhibitory function. Although σ(54) and the major σ factor, σ(70), have similar functional domains and contact similar regions of RNAP, unanticipated differences are observed in their domain arrangement and interactions with RNAP, explaining their distinct properties. Furthermore, we observe evolutionarily conserved regulatory hotspots in RNAPs that can be targeted by a diverse range of mechanisms to fine tune transcription.


    Organizational Affiliation

    Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK. Department of Medicine, Imperial College London, South Kensington SW7 2AZ, UK. xiaodong.zhang@imperial.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaAB329Escherichia coliMutation(s): 0 
Gene Names: rpoAZ4665ECs4160
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Z4
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1342Escherichia coliMutation(s): 0 
Gene Names: rpoBZ5560ECs4910
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Explore P0A8V2 
Go to UniProtKB:  P0A8V2
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1407Escherichia coliMutation(s): 0 
Gene Names: rpoCZ5561ECs4911
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Explore P0A8T7 
Go to UniProtKB:  P0A8T7
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE91Escherichia coliMutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
Explore P0A800 
Go to UniProtKB:  P0A800
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.50 Å
  • R-Value Free: 0.470 
  • R-Value Work: 0.470 
  • R-Value Observed: 0.470 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 255.544α = 90
b = 255.544β = 90
c = 189.392γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence