6GFW

Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme initial transcribing complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation.

Glyde, R.Ye, F.Jovanovic, M.Kotta-Loizou, I.Buck, M.Zhang, X.

(2018) Mol Cell 70: 1111-1120.e3

  • DOI: 10.1016/j.molcel.2018.05.021
  • Primary Citation of Related Structures:  
    6GFW, 6GH5, 6GH6

  • PubMed Abstract: 
  • Gene transcription is carried out by multi-subunit RNA polymerases (RNAPs). Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis ...

    Gene transcription is carried out by multi-subunit RNA polymerases (RNAPs). Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis. Applying cryoelectron microscopy to a unique transcription system using σ 54 N ), the major bacterial variant sigma factor, we capture a new intermediate state at 4.1 Å where promoter DNA is caught at the entrance of the RNAP cleft. Combining with new structures of the open promoter complex and an initial de novo transcribing complex at 3.4 and 3.7 Å, respectively, our studies reveal the dynamics of DNA loading and mechanism of transcription bubble stabilization that involves coordinated, large-scale conformational changes of the universally conserved features within RNAP and DNA. In addition, our studies reveal a novel mechanism of strand separation by σ 54 .


    Organizational Affiliation

    Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK. Electronic address: xiaodong.zhang@imperial.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B329Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
UniProt
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
UniProt
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
UniProt
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
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma-54 factorH [auth M]497Klebsiella pneumoniaeMutation(s): 1 
Gene Names: SM87_03359CP995_28845
EC: 2.7.7.6
UniProt
Find proteins for P06223 (Klebsiella oxytoca)
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Entity ID: 5
MoleculeChainsLengthOrganismImage
nifH promoter template DNAF63Klebsiella pneumoniae
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Entity ID: 6
MoleculeChainsLengthOrganismImage
NifH promoter non-template DNAG63Klebsiella pneumoniae
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  • Entity ID: 8
    MoleculeChainsLengthOrganismImage
    de novo synthesized RNAI [auth R]4Escherichia coli K-12
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    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.70 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N007816

    Revision History  (Full details and data files)

    • Version 1.0: 2018-07-04
      Type: Initial release