8REB

Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 6nt complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis of sigma 54 displacement and promoter escape in bacterial transcription.

Gao, F.Ye, F.Zhang, B.Cronin, N.Buck, M.Zhang, X.

(2024) Proc Natl Acad Sci U S A 121: e2309670120-e2309670120

  • DOI: https://doi.org/10.1073/pnas.2309670120
  • Primary Citation of Related Structures:  
    8RE4, 8REA, 8REB, 8REC, 8RED, 8REE

  • PubMed Abstract: 

    Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated, and in bacteria, transcription initiation is mediated by sigma (σ) factors. σ recruits RNAP to the promoter DNA region, located upstream of the transcription start site (TSS) and facilitates open complex formation, where double-stranded DNA is opened up into a transcription bubble and template strand DNA is positioned inside RNAP for initial RNA synthesis. During initial transcription, RNAP remains bound to σ and upstream DNA, presumably with an enlarging transcription bubble. The release of RNAP from upstream DNA is required for promoter escape and processive transcription elongation. Bacteria sigma factors can be broadly separated into two classes with the majority belonging to the σ 70 class, represented by the σ 70 that regulates housekeeping genes. σ 54 forms a class on its own and regulates stress response genes. Extensive studies on σ 70 have revealed the molecular mechanisms of the σ 70 dependent process while how σ 54 transitions from initial transcription to elongation is currently unknown. Here, we present a series of cryo-electron microscopy structures of the RNAP-σ 54 initial transcribing complexes with progressively longer RNA, which reveal structural changes that lead to promoter escape. Our data show that initially, the transcription bubble enlarges, DNA strands scrunch, reducing the interactions between σ 54 and DNA strands in the transcription bubble. RNA extension and further DNA scrunching help to release RNAP from σ 54 and upstream DNA, enabling the transition to elongation.


  • Organizational Affiliation

    Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, United Kingdom.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaD [auth A],
E [auth B]
321Escherichia 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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UniProt GroupP0A7Z4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaF [auth C]1,341Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'G [auth D]1,373Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaH [auth E]74Escherichia 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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma-54 factorI [auth M]350Klebsiella oxytocaMutation(s): 0 
UniProt
Find proteins for P06223 (Klebsiella oxytoca)
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UniProt GroupP06223
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (43-MER)A [auth N]43Escherichia coli K-12
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*CP*CP*GP*CP*G)-3')B [auth R]6Klebsiella oxytoca
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (52-MER)C [auth T]52Klebsiella oxytoca
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomBB/M011178/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release