7YP9

Cryo-EM structure of Escherichia coli paused complex of transcription termination (TTC-pause)


Experimental Data Snapshot

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

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This is version 1.3 of the entry. See complete history


Literature

Structural basis for intrinsic transcription termination.

You, L.Omollo, E.O.Yu, C.Mooney, R.A.Shi, J.Shen, L.Wu, X.Wen, A.He, D.Zeng, Y.Feng, Y.Landick, R.Zhang, Y.

(2023) Nature 613: 783-789

  • DOI: https://doi.org/10.1038/s41586-022-05604-1
  • Primary Citation of Related Structures:  
    7YP9, 7YPA, 7YPB

  • PubMed Abstract: 

    Efficient and accurate termination is required for gene transcription in all living organisms 1,2 . Cellular RNA polymerases in both bacteria and eukaryotes can terminate their transcription through a factor-independent termination pathway 3,4 -called intrinsic termination transcription in bacteria-in which RNA polymerase recognizes terminator sequences, stops nucleotide addition and releases nascent RNA spontaneously. Here we report a set of single-particle cryo-electron microscopy structures of Escherichia coli transcription intrinsic termination complexes representing key intermediate states of the event. The structures show how RNA polymerase pauses at terminator sequences, how the terminator RNA hairpin folds inside RNA polymerase, and how RNA polymerase rewinds the transcription bubble to release RNA and then DNA. These macromolecular snapshots define a structural mechanism for bacterial intrinsic termination and a pathway for RNA release and DNA collapse that is relevant for factor-independent termination by all RNA polymerases.


  • Organizational Affiliation

    Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8V2
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UniProt GroupP0A8V2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,416Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoC
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 K-12Mutation(s): 0 
Gene Names: rpoZ
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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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (31-MER)31synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (31-MER)31synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*CP*GP*UP*CP*GP*CP*AP*GP*GP*CP*CP*UP*UP*UP*UP*UP*AP*UP*U)-3')20synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14
RECONSTRUCTIONRELION3.08

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references, Refinement description
  • Version 1.2: 2023-01-25
    Changes: Database references
  • Version 1.3: 2023-02-08
    Changes: Database references