7XUG

cryo-EM structure of HK022 putRNA-less E.coli RNA polymerase elongation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA.

Hwang, S.Olinares, P.D.B.Lee, J.Kim, J.Chait, B.T.King, R.A.Kang, J.Y.

(2022) Nat Commun 13: 4668-4668

  • DOI: https://doi.org/10.1038/s41467-022-32315-y
  • Primary Citation of Related Structures:  
    7XUE, 7XUG, 7XUI

  • PubMed Abstract: 

    Transcription, in which RNA polymerases (RNAPs) produce RNA from DNA, is the first step of gene expression. As such, it is highly regulated either by trans-elements like protein factors and/or by cis-elements like specific sequences on the DNA. Lambdoid phage HK022 contains a cis-element, put, which suppresses pausing and termination during transcription of the early phage genes. The putRNA transcript solely performs the anti-pausing/termination activities by interacting directly with the E.coli RNAP elongation complex (EC) by an unknown structural mechanism. In this study, we reconstituted putRNA-associated ECs and determined the structures using cryo-electron microscopy. The determined structures of putRNA-associated EC, putRNA-absent EC, and σ 70 -bound EC suggest that the putRNA interaction with the EC counteracts swiveling, a conformational change previously identified to promote pausing and σ 70 might modulate putRNA folding via σ 70 -dependent pausing during elongation.


  • Organizational Affiliation

    Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaD [auth G],
E [auth H]
329Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoA
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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaF [auth I]1,342Escherichia 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'G [auth J]1,430Escherichia 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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaH [auth K]91Escherichia 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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UniProt GroupP0A800
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Entity ID: 1
MoleculeChains LengthOrganismImage
non-template DNA177Shamshuipovirus HK022
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Entity ID: 2
MoleculeChains LengthOrganismImage
template DNA177Shamshuipovirus HK022
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (nun gene and immunity region)C [auth R]95Shamshuipovirus HK022
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2019R1F1A1064026
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2019M3E5D6066058
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021R1C1C100656011
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM109824
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103314

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2024-07-03
    Changes: Data collection, Refinement description