6XLN

Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.

Yang, Y.Liu, C.Zhou, W.Shi, W.Chen, M.Zhang, B.Schatz, D.G.Hu, Y.Liu, B.

(2021) Nat Commun 12: 2702-2702

  • DOI: https://doi.org/10.1038/s41467-021-22990-8
  • Primary Citation of Related Structures:  
    6WL5, 6XL5, 6XL6, 6XL9, 6XLA, 6XLJ, 6XLK, 6XLL, 6XLM, 6XLN

  • PubMed Abstract: 

    Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of transcriptional regulators activate suboptimal 19-20 bp spacer promoters in response to myriad cellular signals, ranging from heavy metals to drug-like compounds. The regulation of transcription by MerR family regulators is not fully understood. Here we report one crystal structure of a multidrug-sensing MerR family regulator EcmrR and nine cryo-electron microscopy structures that capture the EcmrR-dependent transcription process from promoter opening to initial transcription to RNA elongation. These structures reveal that EcmrR is a dual ligand-binding factor that reshapes the suboptimal 19-bp spacer DNA to enable optimal promoter recognition, sustains promoter remodeling to stabilize initial transcribing complexes, and finally dissociates from the promoter to reverse DNA remodeling and facilitate the transition to elongation. Our findings yield a comprehensive model for transcription regulation by MerR family factors and provide insights into the transition from transcription initiation to elongation.


  • Organizational Affiliation

    Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA. yan9yang@iastate.edu.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoAZ4665ECs4160
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 beta1,342Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoBECS88_4448
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 O157:H7Mutation(s): 0 
Gene Names: rpoCZ5561ECs4911
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 O157:H7Mutation(s): 0 
Gene Names: rpoZECS88_4064
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChains LengthOrganismImage
synthetic non-template strand DNA (54-MER)F [auth N]54Escherichia coli O157:H7
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Entity ID: 6
MoleculeChains LengthOrganismImage
synthetic template strand DNA (54-MER)G [auth T]54Escherichia coli O157:H7
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Entity ID: 7
MoleculeChains LengthOrganismImage
9-nt RNA transcriptH [auth R]9Escherichia coli O157:H7
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16
RECONSTRUCTIONcryoSPARC2.14

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 1.2: 2021-05-26
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Refinement description