7MKI

Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR (-5G to C) promoter DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structural origins of Escherichia coli RNA polymerase open promoter complex stability.

Saecker, R.M.Chen, J.Chiu, C.E.Malone, B.Sotiris, J.Ebrahim, M.Yen, L.Y.Eng, E.T.Darst, S.A.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2112877118
  • Primary Citation of Related Structures:  
    7MKD, 7MKE, 7MKI, 7MKJ

  • PubMed Abstract: 

    The first step in gene expression in all organisms requires opening the DNA duplex to expose one strand for templated RNA synthesis. In Escherichia coli , promoter DNA sequence fundamentally determines how fast the RNA polymerase (RNAP) forms "open" complexes (RPo), whether RPo persists for seconds or hours, and how quickly RNAP transitions from initiation to elongation. These rates control promoter strength in vivo, but their structural origins remain largely unknown. Here, we use cryoelectron microscopy to determine the structures of RPo formed de novo at three promoters with widely differing lifetimes at 37 °C: λP R (t 1/2 ∼10 h), T7A1 (t 1/2 ∼4 min), and a point mutant in λP R (λP R-5C ) (t 1/2 ∼2 h). Two distinct RPo conformers are populated at λP R , likely representing productive and unproductive forms of RPo observed in solution studies. We find that changes in the sequence and length of DNA in the transcription bubble just upstream of the start site (+1) globally alter the network of DNA-RNAP interactions, base stacking, and strand order in the single-stranded DNA of the transcription bubble; these differences propagate beyond the bubble to upstream and downstream DNA. After expanding the transcription bubble by one base (T7A1), the nontemplate strand "scrunches" inside the active site cleft; the template strand bulges outside the cleft at the upstream edge of the bubble. The structures illustrate how limited sequence changes trigger global alterations in the transcription bubble that modulate the RPo lifetime and affect the subsequent steps of the transcription cycle.


  • Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065; rsaecker@rockefeller.edu darst@rockefeller.edu.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaB [auth G],
C [auth H]
329Escherichia coliMutation(s): 0 
Gene Names: rpoA
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD [auth I]1,342Escherichia coliMutation(s): 0 
Gene Names: rpoBZ5560ECs4910
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'E [auth J]1,407Escherichia coliMutation(s): 0 
Gene Names: rpoCBvCmsKKP036_03580
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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaF [auth K]91Escherichia coliMutation(s): 0 
Gene Names: rpoZZ5075ECs4524
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDG [auth L]613Escherichia coliMutation(s): 0 
Gene Names: rpoD
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
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UniProt GroupP00579
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Entity ID: 1
MoleculeChains LengthOrganismImage
Nontemplate strand of lambda PR DNA promoter (-5G to C)A [auth P]90Lambdavirus lambda
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Entity ID: 7
MoleculeChains LengthOrganismImage
Template strand of lambda PR promoter DNA (-5C to G)H [auth Q]90Lambdavirus lambda
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118130

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references