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- EMDB-22886: Mycobacterium tuberculosis WT RNAP transcription open promoter co... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22886 | |||||||||
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Title | Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 transcription factor | |||||||||
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![]() | RNA polymerase / Transcription factor / Mycobacterium tuberculosis / Iron cluster / TRANSCRIPTION / TRANSFERASE-DNA complex | |||||||||
Function / homology | ![]() dinitrosyl-iron complex binding / protein-disulfide reductase (NAD(P)H) activity / bacterial-type RNA polymerase core enzyme binding / response to fatty acid / sigma factor activity / rRNA transcription / DNA-directed RNA polymerase complex / cell redox homeostasis / DNA-templated transcription initiation / ribonucleoside binding ...dinitrosyl-iron complex binding / protein-disulfide reductase (NAD(P)H) activity / bacterial-type RNA polymerase core enzyme binding / response to fatty acid / sigma factor activity / rRNA transcription / DNA-directed RNA polymerase complex / cell redox homeostasis / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 4 iron, 4 sulfur cluster binding / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.94 Å | |||||||||
![]() | Lilic M / Darst SA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7. Authors: Mirjana Lilic / Seth A Darst / Elizabeth A Campbell / ![]() 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 ...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-holoenzyme, global regulators CarD and RbpA, and WhiB7, bound to a WhiB7-regulated promoter. The structures reveal how WhiB7 interacts with σ-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. | |||||||||
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 | ![]() | 86.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.5 KB 23.5 KB | Display Display | ![]() |
Images | ![]() | 23.8 KB | ||
Filedesc metadata | ![]() | 8.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kifMC ![]() 7kimC ![]() 7kinC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 2.0 TB Data #1: Unaligned multi-frame raw micrographs of Mycobacterium tuberculosis RNAP with WhiB7 transcription factor [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Mycobacterium tuberculosis WT RNAP transcription open promoter co...
+Supramolecule #1: Mycobacterium tuberculosis WT RNAP transcription open promoter co...
+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 #7: RNA polymerase-binding transcription factor CarD
+Macromolecule #10: Probable transcriptional regulator WhiB7
+Macromolecule #8: DNA (63-MER)
+Macromolecule #9: DNA (55-MER)
+Macromolecule #11: ZINC ION
+Macromolecule #12: MAGNESIUM ION
+Macromolecule #13: IRON/SULFUR CLUSTER
-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: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 66.0 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
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87743 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |