6ALF

CryoEM structure of crosslinked E.coli RNA polymerase elongation complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


Literature

Structural basis of transcription arrest by coliphage HK022 Nun in anEscherichia coliRNA polymerase elongation complex.

Kang, J.Y., Olinares, P.D., Chen, J., Campbell, E.A., Mustaev, A., Chait, B.T., Gottesman, M.E., Darst, S.A.

(2017) Elife 6

  • DOI: 10.7554/eLife.25478
  • Primary Citation of Related Structures:  
    6ALF, 6ALH, 6ALG

  • PubMed Abstract: 

    • Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λ DNA. To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy ...

    Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λ DNA. To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy. Nun fits tightly into the TEC by taking advantage of gaps between the RNAP and the nucleic acids. The C-terminal segment of Nun interacts with the RNAP β and β' subunits inside the RNAP active site cleft as well as with nearly every element of the nucleic acid scaffold, essentially crosslinking the RNAP and the nucleic acids to prevent translocation, a mechanism supported by the effects of Nun amino acid substitutions. The nature of Nun interactions inside the RNAP active site cleft suggests that RNAP clamp opening is required for Nun to establish its interactions, explaining why Nun acts on paused TECs.

    Organizational Affiliation: 

    Laboratory of Molecular Biophysics, The Rockefeller University, New York City, United States.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaG, H239Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoA, pez, phs, sez, b3295, JW3257
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Z4
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaI1342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8V2
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'J1407Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoC, tabB, b3988, JW3951
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8T7
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaK80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZ, b3649, JW3624
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A800
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*GP*CP*TP*AP*AP*TP*GP*AP*CP*GP*GP*CP*GP*AP*AP*TP*AP*CP*CP*C)-3')A29Escherichia phage T7
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (29-MER)B29Escherichia phage T7
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')R20Escherichia phage T7
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN
    Download Ideal Coordinates CCD File 
    J
    		ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N    		 Ligand Interaction
    MG
    Query on MG
    Download Ideal Coordinates CCD File 
    J
    		MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 4.10 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    View more in-depth experimental data

    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2017-08-07 
    • Released Date: 2017-08-16 
      • Deposition Author(s): Kang, J.Y., Darst, S.A.
    • This entry supersedes: 5UPA
    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118130

    Revision History 

    • Version 1.0: 2017-08-16
      Type: Initial release
    • Version 1.1: 2017-09-20
      Changes: Author supporting evidence, Data collection
    • Version 1.2: 2017-11-08
      Changes: Derived calculations
    • Version 1.3: 2018-02-28
      Changes: Database references, Other, Structure summary
    • Version 1.4: 2018-03-28
      Changes: Data collection, Database references
    • Version 1.5: 2018-07-18
      Changes: Data collection
    • Version 1.6: 2019-12-18
      Changes: Author supporting evidence, Other