6JNX

Cryo-EM structure of a Q-engaged arrested complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of Q-dependent transcription antitermination.

Shi, J.Gao, X.Tian, T.Yu, Z.Gao, B.Wen, A.You, L.Chang, S.Zhang, X.Zhang, Y.Feng, Y.

(2019) Nat Commun 10: 2925-2925

  • DOI: 10.1038/s41467-019-10958-8
  • Primary Citation of Related Structures:  
    6JNY, 6JNX

  • PubMed Abstract: 
  • Bacteriophage Q protein engages σ-dependent paused RNA polymerase (RNAP) by binding to a DNA site embedded in late gene promoter and renders RNAP resistant to termination signals. Here, we report a single-particle cryo-electron microscopy (cryo-EM) structure of an intact Q-engaged arrested complex ...

    Bacteriophage Q protein engages σ-dependent paused RNA polymerase (RNAP) by binding to a DNA site embedded in late gene promoter and renders RNAP resistant to termination signals. Here, we report a single-particle cryo-electron microscopy (cryo-EM) structure of an intact Q-engaged arrested complex. The structure reveals key interactions responsible for σ-dependent pause, Q engagement, and Q-mediated transcription antitermination. The structure shows that two Q protomers (Q I and Q II ) bind to a direct-repeat DNA site and contact distinct elements of the RNA exit channel. Notably, Q I forms a narrow ring inside the RNA exit channel and renders RNAP resistant to termination signals by prohibiting RNA hairpin formation in the RNA exit channel. Because the RNA exit channel is conserved among all multisubunit RNAPs, it is likely to serve as an important contact site for regulators that modify the elongation properties of RNAP in other organisms, as well.


    Organizational Affiliation

    Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China. yufengjay@zju.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B329Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1342Escherichia 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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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1407Escherichia 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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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE91Escherichia 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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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDF613Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoDaltb3067JW3039
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Antiterminator Q proteinJ [auth P], K [auth Q]162Enterobacteria phage SfIMutation(s): 0 
Gene Names: QSfI_0061
UniProt
Find proteins for M1FPN0 (Enterobacteria phage SfI)
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (63-MER)G [auth N]63Enterobacteria phage P21
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  • Entity ID: 7
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*AP*UP*AP*AP*GP*GP*UP*GP*GP*GP*GP*UP*UP*AP*GP*UP*GP*A)-3')H [auth R]18Enterobacteria phage P21
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    Entity ID: 8
    MoleculeChainsLengthOrganismImage
    DNA (63-MER)I [auth T]63Enterobacteria phage P21
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    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    M [auth D], N [auth D]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    L [auth D]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 4.08 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    • Deposited Date: 2019-03-18 
    • Released Date: 2019-06-12 
    • Deposition Author(s): Feng, Y., Shi, J.

    Revision History  (Full details and data files)

    • Version 1.0: 2019-06-12
      Type: Initial release
    • Version 1.1: 2019-07-17
      Changes: Data collection, Database references
    • Version 1.2: 2019-11-06
      Changes: Data collection, Other