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: https://doi.org/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 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

    Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraβe 6, D-14195 Berlin, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antitermination protein NA [auth N]85Lambdavirus lambdaMutation(s): 0 
Gene Names: Nlambdap49
UniProt
Find proteins for P03045 (Escherichia phage lambda)
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UniProt GroupP03045
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaC [auth A],
D [auth B]
329Escherichia coliMutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaE [auth C]1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoBgroNnitBrifronstlstvtabDb3987JW3950
EC: 2.7.7.6
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'F [auth D]1,416Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10G [auth E]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusGH [auth F]183Escherichia coli K-12Mutation(s): 0 
Gene Names: nusGb3982JW3945
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription antitermination protein NusB139Escherichia coli K-12Mutation(s): 0 
Gene Names: nusBgroNBssyBb0416JW0406
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusA497Escherichia coli K-12Mutation(s): 0 
Gene Names: nusAb3169JW3138
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaN [auth O]91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
UniProt
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Entity ID: 2
MoleculeChains LengthOrganismImage
nascent RNAB [auth R]29Escherichia coli
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Entity ID: 8
MoleculeChains LengthOrganismImage
RNA transcription bubbleI [auth H]14Escherichia coli
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNAIJ [auth I]27Escherichia coli
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Entity ID: 10
MoleculeChains LengthOrganismImage
DNAIIK [auth J]39Escherichia coli
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Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB740

Revision History  (Full details and data files)

  • 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