+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13205 | |||||||||
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Title | Mycobacterial RNAP with transcriptional activator PafBC | |||||||||
Map data | full map, sharpened | |||||||||
Sample |
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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 | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Mueller AU / Kummer E | |||||||||
Funding support | Switzerland, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13205.map.gz | 230.1 MB | EMDB map data format | |
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Header (meta data) | emd-13205-v30.xml emd-13205.xml | 28.6 KB 28.6 KB | Display Display | EMDB header |
Images | emd_13205.png | 148.9 KB | ||
Masks | emd_13205_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-13205.cif.gz | 8.8 KB | ||
Others | emd_13205_additional_1.map.gz emd_13205_half_map_1.map.gz emd_13205_half_map_2.map.gz | 122.5 MB 226.9 MB 226.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13205 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13205 | HTTPS FTP |
-Validation report
Summary document | emd_13205_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_13205_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_13205_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_13205_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13205 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13205 | HTTPS FTP |
-Related structure data
Related structure data | 7p5xMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13205.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
File | emd_13205_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: full map, unsharpened
File | emd_13205_additional_1.map | ||||||||||||
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Annotation | full map, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13205_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13205_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : DNA-directed RNA polymerase with transcriptional activator PafBC
+Supramolecule #1: DNA-directed RNA polymerase with transcriptional activator PafBC
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #5: RNA polymerase sigma factor SigA
+Macromolecule #6: RNA polymerase-binding protein RbpA
+Macromolecule #9: PafC
+Macromolecule #10: Transcriptional regulator-like protein
+Macromolecule #7: recA-op non-template strand
+Macromolecule #8: recA-op template strand
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128190 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |