6TYG

Crystal structure of MTB sigma L transcription initiation complex with 9 nt long RNA primer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.

Li, L.Molodtsov, V.Lin, W.Ebright, R.H.Zhang, Y.

(2020) Proc Natl Acad Sci U S A 117: 5801-5809

  • DOI: 10.1073/pnas.1920747117
  • Primary Citation of Related Structures:  
    6TYF, 6TYE, 6TYG, 6L74, 6KOO, 6KON, 6KOQ, 6KOP, 6KQM, 6KQL, 6KQN, 6KQE, 6KQD, 6KQG, 6KQF, 6KQH, 6LTS

  • PubMed Abstract: 
  • All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center ...

    All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. The structures reveal that-for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "σ-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ∼5 nt to ∼10 nt.


    Related Citations: 
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., Adams, P.D.
      (2012) Acta Crystallogr D Biol Crystallogr 68: 352
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C., Zwart, P.H.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 213

    Organizational Affiliation

    Department of Chemistry, Rutgers University, Piscataway, NJ 08854.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factorA [auth F]177Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P9WGH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaE [auth A], F [auth B]347Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
UniProt
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaG [auth C]1178Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
UniProt
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'H [auth D]1316Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 2.7.7.6
UniProt
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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  • Reference Sequence
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaI [auth E]110Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Go to UniProtKB:  P9WGY5
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*AP*TP*CP*GP*AP*GP*GP*GP*TP*G)-3')B [auth G]20Mycobacterium tuberculosis
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    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*TP*GP*TP*CP*AP*GP*TP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*C)-3')C [auth H]27Mycobacterium tuberculosis
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    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(P*CP*AP*CP*CP*CP*UP*CP*GP*A)-3')D [auth I]9Mycobacterium tuberculosis
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.50 Å
      • R-Value Free: 0.293 
      • R-Value Work: 0.246 
      • R-Value Observed: 0.248 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 128.65α = 90
      b = 158.227β = 90
      c = 215.249γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      HKL-3000phasing

      Structure Validation

      View Full Validation Report




      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

      Revision History  (Full details and data files)

      • Version 1.0: 2020-03-11
        Type: Initial release
      • Version 1.1: 2020-03-25
        Changes: Database references