8EHI

Cryo-EM structure of his-elemental paused elongation complex with an unfolded TL (2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.

Kang, J.Y.Mishanina, T.V.Bao, Y.Chen, J.Llewellyn, E.Liu, J.Darst, S.A.Landick, R.

(2023) Proc Natl Acad Sci U S A 120: e2215945120-e2215945120

  • DOI: https://doi.org/10.1073/pnas.2215945120
  • Primary Citation of Related Structures:  
    8EG7, 8EG8, 8EGB, 8EH8, 8EH9, 8EHA, 8EHF, 8EHI

  • PubMed Abstract: 

    Transcriptional pausing underpins the regulation of cellular RNA synthesis, but its mechanism remains incompletely understood. Sequence-specific interactions of DNA and RNA with the dynamic, multidomain RNA polymerase (RNAP) trigger reversible conformational changes at pause sites that temporarily interrupt the nucleotide addition cycle. These interactions initially rearrange the elongation complex (EC) into an elemental paused EC (ePEC). ePECs can form longer-lived PECs by further rearrangements or interactions of diffusible regulators. For both bacterial and mammalian RNAPs, a half-translocated state in which the next DNA template base fails to load into the active site appears central to the ePEC. Some RNAPs also swivel interconnected modules that may stabilize the ePEC. However, it is unclear whether swiveling and half-translocation are requisite features of a single ePEC state or if multiple ePEC states exist. Here, we use cryo-electron microscopy (cryo-EM) analysis of ePECs with different RNA-DNA sequences combined with biochemical probes of ePEC structure to define an interconverting ensemble of ePEC states. ePECs occupy either pre- or half-translocated states but do not always swivel, indicating that difficulty in forming the posttranslocated state at certain RNA-DNA sequences may be the essence of the ePEC. The existence of multiple ePEC conformations has broad implications for transcriptional regulation.


  • Organizational Affiliation

    Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, 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]
239Escherichia coliMutation(s): 0 
Gene Names: rpoAZ4665ECs4160
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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaF [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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'G [auth J]1,407Escherichia coliMutation(s): 0 
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 coliMutation(s): 0 
Gene Names: rpoZZ5075ECs4524
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A800
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UniProt GroupP0A800
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Entity ID: 1
MoleculeChains LengthOrganismImage
non-template DNA32Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
template DNA32Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNAC [auth R]19Escherichia coli
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

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 StatesGM118130
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM38330

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection, Refinement description