5MS0

pseudo-atomic model of the RNA polymerase lambda-based antitermination complex solved by cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.80 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 for lambda N-dependent processive transcription antitermination.

Said, N.Krupp, F.Anedchenko, E.Santos, K.F.Dybkov, O.Huang, Y.H.Lee, C.T.Loll, B.Behrmann, E.Burger, J.Mielke, T.Loerke, J.Urlaub, H.Spahn, C.M.T.Weber, G.Wahl, M.C.

(2017) Nat Microbiol 2: 17062-17062

  • DOI: 10.1038/nmicrobiol.2017.62
  • Primary Citation of Related Structures:  
    5LM7, 5LM9, 5MS0

  • PubMed Abstract: 
  • λN-mediated processive antitermination constitutes a paradigmatic transcription regulatory event, during which phage protein λN, host factors NusA, NusB, NusE and NusG, and an RNA nut site render elongating RNA polymerase termination-resistant. The s ...

    λN-mediated processive antitermination constitutes a paradigmatic transcription regulatory event, during which phage protein λN, host factors NusA, NusB, NusE and NusG, and an RNA nut site render elongating RNA polymerase termination-resistant. The structural basis of the process has so far remained elusive. Here we describe a crystal structure of a λN-NusA-NusB-NusE-nut site complex and an electron cryo-microscopic structure of a complete transcription antitermination complex, comprising RNA polymerase, DNA, nut site RNA, all Nus factors and λN, validated by crosslinking/mass spectrometry. Due to intrinsic disorder, λN can act as a multiprotein/RNA interaction hub, which, together with nut site RNA, arranges NusA, NusB and NusE into a triangular complex. This complex docks via the NusA N-terminal domain and the λN C-terminus next to the RNA exit channel on RNA polymerase. Based on the structures, comparative crosslinking analyses and structure-guided mutagenesis, we hypothesize that λN mounts a multipronged strategy to reprogram the transcriptional machinery, which may include (1) the λN C terminus clamping the RNA exit channel, thus stabilizing the DNA:RNA hybrid; (2) repositioning of NusA and RNAP elements, thus redirecting nascent RNA and sequestering the upstream branch of a terminator hairpin; and (3) hindering RNA engagement of termination factor ρ and/or obstructing ρ translocation on the transcript.


    Organizational Affiliation

    Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, D-12489 Berlin, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antitermination protein NN85Escherichia virus LambdaMutation(s): 0 
Gene Names: Nlambdap49
Find proteins for P03045 (Escherichia phage lambda)
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Go to UniProtKB:  P03045
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaAB329Escherichia coliMutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoBgroNnitBrifronstlstvtabDb3987JW3950
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1416Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10E100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
Find proteins for P0A7R5 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusGF183Escherichia coli K-12Mutation(s): 0 
Gene Names: nusGb3982JW3945
Find proteins for P0AFG0 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription antitermination protein NusBL139Escherichia coli K-12Mutation(s): 0 
Gene Names: nusBgroNBssyBb0416JW0406
Find proteins for P0A780 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusAM497Escherichia coli K-12Mutation(s): 0 
Gene Names: nusAb3169JW3138
Find proteins for P0AFF6 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaO91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
nascent RNAR29Escherichia coli
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  • Entity ID: 8
    MoleculeChainsLengthOrganismImage
    RNA transcription bubbleH14Escherichia coli
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    Entity ID: 9
    MoleculeChainsLengthOrganismImage
    DNAII27Escherichia coli
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    Entity ID: 10
    MoleculeChainsLengthOrganismImage
    DNAIIJ39Escherichia coli
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    D
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 9.80 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2016-12-29 
    • Released Date: 2017-05-03 
    • Deposition Author(s): Said, N., Krupp, F.

    Funding OrganizationLocationGrant Number
    German Research FoundationGermanySFB740

    Revision History 

    • Version 1.0: 2017-05-03
      Type: Initial release
    • Version 1.1: 2017-05-10
      Changes: Database references
    • Version 1.2: 2018-10-31
      Changes: Author supporting evidence, Data collection, Database references, Source and taxonomy, Structure summary