+Open data
-Basic information
Entry | Database: PDB / ID: 7p5x | ||||||
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Title | Mycobacterial RNAP with transcriptional activator PafBC | ||||||
Components |
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Keywords | TRANSCRIPTION / activator / sigma adaption / RNA polymerase / RNAP / PafB / PafC / PafBC / Mycobacterium / smegmatis | ||||||
Function / homology | Function and homology information bacterial-type RNA polymerase core enzyme binding / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription ...bacterial-type RNA polymerase core enzyme binding / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Mueller, A.U. / Kummer, E. / Schilling, C.M. / Ban, N. / Weber-Ban, E. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Sci Adv / Year: 2021 Title: Transcriptional control of mycobacterial DNA damage response by sigma adaptation. Authors: Andreas U Müller / Eva Kummer / Charlotte M Schilling / Nenad Ban / Eilika Weber-Ban / 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 ...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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7p5x.cif.gz | 685.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p5x.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7p5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/7p5x ftp://data.pdbj.org/pub/pdb/validation_reports/p5/7p5x | HTTPS FTP |
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-Related structure data
Related structure data | 13205MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules AAABACADAE
#1: Protein | Mass: 37959.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0QSL8, DNA-directed RNA polymerase #2: Protein | | Mass: 128680.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P60281, DNA-directed RNA polymerase #3: Protein | | Mass: 146712.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0QS66 #4: Protein | | Mass: 11544.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QWT1, DNA-directed RNA polymerase |
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-Protein , 4 types, 4 molecules AFAJAXAY
#5: Protein | Mass: 51573.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: sigA, MSMEG_2758 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QW02 |
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#6: Protein | Mass: 13078.731 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: rbpA, MSMEG_3858, MSMEI_3768 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QZ11 |
#9: Protein | Mass: 34044.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: residues 82-123 have been modelled as poly-alanine Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_3888 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QZ41 |
#10: Protein | Mass: 36081.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: residues 84-128 have been modelled as poly-alanine Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: pafB, MSMEI_3799 / Production host: Escherichia coli (E. coli) / References: UniProt: I7G3U5 |
-DNA chain , 2 types, 2 molecules AOAP
#7: DNA chain | Mass: 23733.148 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Mycolicibacterium smegmatis MC2 155 (bacteria) |
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#8: DNA chain | Mass: 23746.215 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Mycolicibacterium smegmatis MC2 155 (bacteria) |
-Non-polymers , 1 types, 2 molecules
#11: Chemical |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DNA-directed RNA polymerase with transcriptional activator PafBC Type: COMPLEX / Entity ID: #1-#10 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128190 / Symmetry type: POINT |