6CA0

Cryo-EM structure of E. coli RNAP sigma70 open complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure ofEscherichia colisigma70RNA polymerase and promoter DNA complex revealed a role of sigma non-conserved region during the open complex formation.

Narayanan, A.Vago, F.S.Li, K.Qayyum, M.Z.Yernool, D.Jiang, W.Murakami, K.S.

(2018) J Biol Chem 293: 7367-7375

  • DOI: 10.1074/jbc.RA118.002161
  • Primary Citation of Related Structures:  
    6C9Y, 6CA0

  • PubMed Abstract: 
  • First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In Escherichia coli , a primary σ 70 factor forms the RNAP holoenzyme to ex ...

    First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In Escherichia coli , a primary σ 70 factor forms the RNAP holoenzyme to express housekeeping genes. The σ 70 contains a large insertion between the conserved regions 1.2 and 2.1, the σ non-conserved region (σ NCR ), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP σ 70 holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between the σ NCR and promoter DNA just upstream of the -10 element, which was not observed in a previously determined E. coli RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of the σ NCR and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the σ NCR and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802 and kum14@psu.edu.



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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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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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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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDF613Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoDaltb3067JW3039
Find proteins for P00579 (Escherichia coli (strain K12))
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (45-MER)G45Escherichia coli K-12
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (35-MER)H35Escherichia coli K-12
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  • Entity ID: 8
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*CP*TP*GP*AP*CP*GP*CP*GP*GP*C)-3')I11Escherichia coli K-12
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    • Entity ID: 9
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*GP*CP*CP*GP*CP*GP*TP*CP*AP*GP*A)-3')J11Escherichia coli K-12
      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

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      D
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 5.75 Å
      • Aggregation State: PARTICLE 
      • Reconstruction Method: SINGLE PARTICLE 

      Structure Validation

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      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM087350
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM093142

      Revision History 

      • Version 1.0: 2018-02-28
        Type: Initial release
      • Version 1.1: 2018-10-24
        Changes: Data collection, Database references
      • Version 1.2: 2020-01-08
        Changes: Author supporting evidence