6DVB

Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 5nt spacer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of ECF-sigma-factor-dependent transcription initiation.

Lin, W.Mandal, S.Degen, D.Cho, M.S.Feng, Y.Das, K.Ebright, R.H.

(2019) Nat Commun 10: 710-710

  • DOI: 10.1038/s41467-019-08443-3
  • Primary Citation of Related Structures:  
    6DV9, 6DVB, 6DVC, 6DVD, 6DVE

  • PubMed Abstract: 
  • Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of six conserved functional modules in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M ...

    Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of six conserved functional modules in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF σ factor σ L , and promoter DNA. The structures show that σR2 and σR4 of the ECF σ factor occupy the same sites on RNAP as in primary σ factors, show that the connector between σR2 and σR4 of the ECF σ factor-although shorter and unrelated in sequence-follows the same path through RNAP as in primary σ factors, and show that the ECF σ factor uses the same strategy to bind and unwind promoter DNA as primary σ factors. The results define protein-protein and protein-DNA interactions involved in ECF-σ-factor-dependent transcription initiation.


    Organizational Affiliation

    Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ, 08854, USA. ebright@waksman.rutgers.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B359Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoARv3457cMTCY13E12.10c
EC: 2.7.7.6
UniProt
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Go to UniProtKB:  P9WGZ1
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1178Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoBRv0667MTCI376.08c
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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1316Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoCRv0668MTCI376.07c
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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE110Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoZRv1390MTCY21B4.07
EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ECF RNA polymerase sigma factor SigLF177Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: sigLRv0735
UniProt
Find proteins for P9WGH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 6
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*CP*UP*CP*GP*A)-3')G [auth I]5Mycobacterium tuberculosis H37Rv
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 7
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*G)-3')H [auth G]17Mycobacterium tuberculosis H37Rv
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      Entity ID: 8
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*GP*TP*GP*TP*CP*AP*GP*TP*AP*GP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*C)-3')I [auth H]23Mycobacterium tuberculosis H37Rv
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      J [auth D], K [auth D]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.80 Å
      • R-Value Free: 0.241 
      • R-Value Work: 0.202 
      • R-Value Observed: 0.203 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 143.658α = 90
      b = 160.58β = 90
      c = 240.37γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      Aimlessdata scaling
      PDB_EXTRACTdata extraction
      iMOSFLMdata reduction
      PHENIXphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2019-02-20
        Type: Initial release
      • Version 1.1: 2019-02-27
        Changes: Data collection, Database references