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 

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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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,342Escherichia 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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UniProt GroupP0A8V2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,407Escherichia 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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UniProt GroupP0A8T7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega91Escherichia 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
MoleculeChains Sequence 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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UniProt GroupP06223
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Entity ID: 5
MoleculeChains LengthOrganismImage
nifH promoter template DNA63Klebsiella pneumoniae
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Entity ID: 6
MoleculeChains LengthOrganismImage
NifH promoter non-template DNA63Klebsiella pneumoniae
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Entity ID: 8
MoleculeChains LengthOrganismImage
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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.10.1
MODEL REFINEMENTCCP4 package7

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
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references