7P5X

Mycobacterial RNAP with transcriptional activator PafBC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Transcriptional control of mycobacterial DNA damage response by sigma adaptation.

Muller, A.U.Kummer, E.Schilling, C.M.Ban, N.Weber-Ban, E.

(2021) Sci Adv 7: eabl4064-eabl4064

  • DOI: https://doi.org/10.1126/sciadv.abl4064
  • Primary Citation of Related Structures:  
    7P5X

  • PubMed Abstract: 

    Transcriptional activator PafBC is the key regulator of the mycobacterial DNA damage response and controls around 150 genes, including genes involved in the canonical SOS response, through an unknown molecular mechanism. Using a combination of biochemistry and cryo–electron microscopy, we demonstrate that PafBC in the presence of single-stranded DNA activates transcription by reprogramming the canonical −10 and −35 promoter specificity of RNA polymerase associated with the housekeeping sigma subunit. We determine the structure of this transcription initiation complex, revealing a unique mode of promoter recognition, which we term “sigma adaptation.” PafBC inserts between DNA and sigma factor to mediate recognition of hybrid promoters lacking the −35 but featuring the canonical −10 and a PafBC-specific −26 element. Sigma adaptation may constitute a more general mechanism of transcriptional control in mycobacteria.


  • Organizational Affiliation

    ETH Zurich, Institute of Molecular Biology and Biophysics, CH-8093 Zurich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA [auth AA],
B [auth AB]
350Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QSL8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC [auth AC]1,169Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupP60281
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D [auth AD]1,317Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0QS66 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QS66
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE [auth AE]107Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAF [auth AF]466Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: sigAMSMEG_2758
UniProt
Find proteins for A0QW02 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpAG [auth AJ]114Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rbpAMSMEG_3858MSMEI_3768
UniProt
Find proteins for A0QZ11 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PafCJ [auth AX]318Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_3888
UniProt
Find proteins for A0QZ41 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator-like proteinK [auth AY]331Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: pafBMSMEI_3799
UniProt
Find proteins for I7G3U5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupI7G3U5
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Entity ID: 7
MoleculeChains LengthOrganismImage
recA-op non-template strandH [auth AO]77Mycolicibacterium smegmatis MC2 155
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Entity ID: 8
MoleculeChains LengthOrganismImage
recA-op template strandI [auth AP]77Mycolicibacterium smegmatis MC2 155
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_185250

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Data collection