6JCY

Mycobacterium tuberculosis RNA polymerase transcription initiation open complex with a chimeric ECF sigma factor sigH/E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

Starting Model: experimental
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Literature

Structures and mechanism of transcription initiation by bacterial ECF factors.

Fang, C.Li, L.Shen, L.Shi, J.Wang, S.Feng, Y.Zhang, Y.

(2019) Nucleic Acids Res 47: 7094-7104

  • DOI: https://doi.org/10.1093/nar/gkz470
  • Primary Citation of Related Structures:  
    6JBQ, 6JCX, 6JCY

  • PubMed Abstract: 

    Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 Å of Escherichia coli transcription initiation complex comprising σE-the most-studied bacterial ECF σ factor (Ec σE-RPo), and a crystal structure at 3.1 Å of Mycobacterium tuberculosis transcription initiation complex with a chimeric σH/E (Mtb σH/E-RPo). The structure of Ec σE-RPo reveals key interactions essential for assembly of E. coli σE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli σE. Moreover, both structures show that the non-conserved linkers (σ2/σ4 linker) of the two ECF σ factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF σ factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such σ2/σ4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF σ factors-mediated transcription initiation.


  • Organizational Affiliation

    Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
368Mycobacterium tuberculosis H37RvMutation(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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UniProt GroupP9WGZ1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,174Mycobacterium tuberculosis H37RvMutation(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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UniProt GroupP9WGY9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,317Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoC
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: rpoZ
EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WGY5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ECF RNA polymerase sigma factor SigH,ECF RNA polymerase sigma factor SigE,ECF RNA polymerase sigma factor SigH209Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: sigHsigE
UniProt
Find proteins for P9WGH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Find proteins for P9WGG7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupsP9WGH9P9WGG7
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*GP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*A)-3')23synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*GP*T)-3')20synthetic construct
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Entity ID: 8
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*CP*UP*CP*GP*A)-3')6synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.943α = 90
b = 163.005β = 117.81
c = 129.315γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670067

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description