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- EMDB-13204: transcriptional activator PafBC bound to mycobacterial RNA polymerase -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13204 | |||||||||
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Title | transcriptional activator PafBC bound to mycobacterial RNA polymerase | |||||||||
![]() | full map, sharpened | |||||||||
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Function / homology | PafC, HTH domain / PafC helix-turn-helix domain / Protein PafC / WYL domain / WYL domain / Protein pafC / Transcriptional regulator-like protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
![]() | Mueller AU / Kummer E / Schilling CM / Ban N / Weber-Ban E | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 228.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.1 KB 18.1 KB | Display Display | ![]() |
Images | ![]() | 106.1 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Others | ![]() ![]() ![]() | 120.2 MB 226.3 MB 226.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 625.5 KB | Display | ![]() |
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Full document | ![]() | 625.1 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | full map, sharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: full map, unsharpened
File | emd_13204_additional_1.map | ||||||||||||
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Annotation | full map, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_13204_half_map_1.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_13204_half_map_2.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : DNA-directed RNA polymerase with transcriptional activator PafBC
Entire | Name: DNA-directed RNA polymerase with transcriptional activator PafBC |
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Components |
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-Supramolecule #1: DNA-directed RNA polymerase with transcriptional activator PafBC
Supramolecule | Name: DNA-directed RNA polymerase with transcriptional activator PafBC type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 |
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-Supramolecule #2: DNA-dependent RNA polymerase
Supramolecule | Name: DNA-dependent RNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: RNA polymerase sigma factor SigA, RNA polymerase-binding protein ...
Supramolecule | Name: RNA polymerase sigma factor SigA, RNA polymerase-binding protein RbpA and RNA polymerase-binding transcription factor CarD type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#8 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #4: PafB and PafC
Supramolecule | Name: PafB and PafC / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #9-#10 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30575 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |