5NWT

Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Holoenzyme complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.76 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.313 
  • R-Value Observed: 0.316 

wwPDB Validation   3D Report Full Report



Literature

TRANSCRIPTION. Structures of the RNA polymerase-Sigma54 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, 5EZK, 5NWT

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaAB329Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
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 coli K-12Mutation(s): 0 
Gene Names: rpoBgroNnitBrifronstlstvtabDb3987JW3950
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1407Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factorM477Klebsiella pneumoniae subsp. rhinoscleromatis SB3432Mutation(s): 0 
Gene Names: rpoNKPR_4804
Find proteins for R4YEY9 (Klebsiella pneumoniae subsp. rhinoscleromatis SB3432)
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
ML-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.76 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.313 
  • R-Value Observed: 0.316 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.477α = 90
b = 151.525β = 90
c = 195.279γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release