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 

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This is version 1.2 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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
359Mycobacterium 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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UniProt GroupP9WGZ1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,178Mycobacterium 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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UniProt GroupP9WGY9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,316Mycobacterium 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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UniProt GroupP9WGY7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega110Mycobacterium 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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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ECF RNA polymerase sigma factor SigL177Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: sigLRv0735
UniProt
Find proteins for P9WGH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WGH5
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*UP*CP*GP*A)-3')G [auth I]5Mycobacterium tuberculosis H37Rv
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Entity ID: 7
MoleculeChains LengthOrganismImage
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
MoleculeChains LengthOrganismImage
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
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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

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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
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references