7KHE

Escherichia coli RNA polymerase and rrnBP1 promoter pre-open complex with DksA/ppGpp

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis of ribosomal RNA transcription regulation.

Shin, Y., Qayyum, M.Z., Pupov, D., Esyunina, D., Kulbachinskiy, A., Murakami, K.S.

(2021) Nat Commun 12: 528-528

  • DOI: 10.1038/s41467-020-20776-y
  • Primary Citation of Related Structures:  
    7KHB, 7KHC, 7KHE, 7KHI

  • PubMed Abstract: 

    • Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ 70 holoenzyme during rRNA promoter recognition with and without DksA/ppGpp ...

    Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ 70 holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ 1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ 1.1 ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA. kum14@psu.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B236Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoA, pez, phs, sez, b3295, JW3257
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
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1,407Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoC, tabB, b3988, JW3951
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZ, b3649, JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDF613Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoD, alt, b3067, JW3039
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding transcription factor DksAI [auth M]151Escherichia coli K-12Mutation(s): 0 
Gene Names: dksA, b0145, JW0141
UniProt
Find proteins for P0ABS1 (Escherichia coli (strain K12))
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UniProt GroupP0ABS1
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (54-MER)G [auth X]61Escherichia coli K-12
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (46-MER)H [auth Y]61Escherichia coli K-12
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 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 StatesGM087350
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131860

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references