8HKC

Cryo-EM structure of E. coli RNAP sigma32 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Insight into the Mechanism of sigma 32-Mediated Transcription Initiation of Bacterial RNA Polymerase.

Lu, Q.Chen, T.Wang, J.Wang, F.Ye, W.Ma, L.Wu, S.

(2023) Biomolecules 13

  • DOI: https://doi.org/10.3390/biom13050738
  • Primary Citation of Related Structures:  
    8HKC

  • PubMed Abstract: 

    Bacterial RNA polymerases (RNAP) form distinct holoenzymes with different σ factors to initiate diverse gene expression programs. In this study, we report a cryo-EM structure at 2.49 Å of RNA polymerase transcription complex containing a temperature-sensitive bacterial σ factor, σ 32 32 -RPo). The structure of σ 32 -RPo reveals key interactions essential for the assembly of E. coli σ 32 -RNAP holoenzyme and for promoter recognition and unwinding by σ 32 . Specifically, a weak interaction between σ 32 and -35/-10 spacer is mediated by T128 and K130 in σ 32 . A histidine in σ 32 , rather than a tryptophan in σ 70 , acts as a wedge to separate the base pair at the upstream junction of the transcription bubble, highlighting the differential promoter-melting capability of different residue combinations. Structure superimposition revealed relatively different orientations between βFTH and σ 4 from other σ-engaged RNAPs and biochemical data suggest that a biased σ 4 -βFTH configuration may be adopted to modulate binding affinity to promoter so as to orchestrate the recognition and regulation of different promoters. Collectively, these unique structural features advance our understanding of the mechanism of transcription initiation mediated by different σ factors.


  • Organizational Affiliation

    State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
331Escherichia 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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UniProt GroupP0A7Z4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,346Escherichia 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'D [auth F]1,425Escherichia 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoHG [auth E]284Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoHfamhinhtpRb3461JW3426
UniProt
Find proteins for P0AGB3 (Escherichia coli (strain K12))
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UniProt GroupP0AGB3
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (54-MER)E [auth G]54Escherichia coli
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (54-MER)F [auth H]54Escherichia coli
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2024-07-03
    Changes: Data collection