5LM7

Crystal structure of the lambda N-Nus factor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.299 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 structural basis of the process has so far remained elusive ...

    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
Transcription termination/antitermination protein NusAA, F [auth C]428Escherichia coli O157:H7Mutation(s): 0 
Gene Names: nusAZ4530ECs4050
Find proteins for P0AFF8 (Escherichia coli O157:H7)
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Go to UniProtKB:  P0AFF8
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N utilization substance protein B homologB, G [auth D]141Escherichia coli S88Mutation(s): 0 
Gene Names: nusBECS88_0411
Find proteins for B7MD74 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Go to UniProtKB:  B7MD74
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10H [auth E], C [auth J]108Escherichia coli S88Mutation(s): 0 
Gene Names: rpsJECS88_3708
Find proteins for B7MCT6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Go to UniProtKB:  B7MCT6
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Antitermination protein NI [auth F], D [auth N]89Escherichia 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: 5
MoleculeChainsLengthOrganismImage
RNA (29-MER)E [auth R], J [auth G]30Escherichia virus Lambda
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.299 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.776α = 90
b = 101.803β = 90
c = 279.918γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references