7KIM

Mycobacterium tuberculosis WT RNAP transcription closed promoter complex with WhiB7 transcription factor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7.

Lilic, M.Darst, S.A.Campbell, E.A.

(2021) Mol Cell 81: 2875-2886.e5

  • DOI: https://doi.org/10.1016/j.molcel.2021.05.017
  • Primary Citation of Related Structures:  
    7KIF, 7KIM, 7KIN

  • PubMed Abstract: 

    In pathogenic mycobacteria, transcriptional responses to antibiotics result in induced antibiotic resistance. WhiB7 belongs to the Actinobacteria-specific family of Fe-S-containing transcription factors and plays a crucial role in inducible antibiotic resistance in mycobacteria. Here, we present cryoelectron microscopy structures of Mycobacterium tuberculosis transcriptional regulatory complexes comprising RNA polymerase σ A -holoenzyme, global regulators CarD and RbpA, and WhiB7, bound to a WhiB7-regulated promoter. The structures reveal how WhiB7 interacts with σ A -holoenzyme while simultaneously interacting with an AT-rich sequence element via its AT-hook. Evidently, AT-hooks, rare elements in bacteria yet prevalent in eukaryotes, bind to target AT-rich DNA sequences similarly to the nuclear chromosome binding proteins. Unexpectedly, a subset of particles contained a WhiB7-stabilized closed promoter complex, revealing this intermediate's structure, and we apply kinetic modeling and biochemical assays to rationalize how WhiB7 activates transcription. Altogether, our work presents a comprehensive view of how WhiB7 serves to activate gene expression leading to antibiotic resistance.


  • Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, 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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UniProt GroupP9WGZ1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,172Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoBMRA_0676
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'1,318Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoCE5M52_05480ERS007665_00591ERS013471_00574ERS023446_00410ERS075361_00813ERS094182_01340F6W99_03342
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 tuberculosisMutation(s): 0 
Gene Names: rpoZERS007703_04032ERS007720_04749ERS094182_01030
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
RNA polymerase sigma factor SigA528Mycobacterium tuberculosisMutation(s): 0 
Gene Names: sigAERDMAN_2966
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpAG [auth J]111Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rbpA
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-binding transcription factor CarDH [auth M]162Mycobacterium tuberculosisMutation(s): 0 
Gene Names: carD
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Probable transcriptional regulator WhiB7K [auth Z]92Mycobacterium tuberculosisMutation(s): 0 
Gene Names: whiB7Rv3197ARv3197.1
UniProt
Find proteins for Q6MX01 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (45-MER)I [auth O]100Mycobacterium tuberculosis
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (45-MER)J [auth P]100Mycobacterium tuberculosis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection