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- PDB-7kim: Mycobacterium tuberculosis WT RNAP transcription closed promoter ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kim | ||||||
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Title | Mycobacterium tuberculosis WT RNAP transcription closed promoter complex with WhiB7 transcription factor | ||||||
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![]() | TRANSCRIPTION / TRANSFERASE/DNA / RNA polymerase / Transcription factor / Mycobacterium tuberculosis / Iron cluster / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å | ||||||
![]() | Lilic, M. / Darst, S.A. / Campbell, E.A. | ||||||
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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 686.2 KB | Display | ![]() |
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PDB format | ![]() | 538.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 22887MC ![]() 7kifC ![]() 7kinC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 37745.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 129372.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | | Mass: 147097.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rpoC, E5M52_05480, ERS007665_00591, ERS013471_00574, ERS023446_00410, ERS075361_00813, ERS094182_01340, F6W99_03342 Production host: ![]() ![]() References: UniProt: A0A045J9E2, DNA-directed RNA polymerase #4: Protein | | Mass: 11819.075 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rpoZ, ERS007703_04032, ERS007720_04749, ERS094182_01030 Production host: ![]() ![]() References: UniProt: A0A0T9N9K3, DNA-directed RNA polymerase |
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-Protein , 2 types, 2 molecules FZ
#5: Protein | Mass: 57845.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#10: Protein | Mass: 10153.804 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-RNA polymerase-binding ... , 2 types, 2 molecules JM
#6: Protein | Mass: 12993.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#7: Protein | Mass: 17933.361 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules OP
#8: DNA chain | Mass: 30844.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#9: DNA chain | Mass: 30862.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 3 types, 4 molecules ![](data/chem/img/ZN.gif)
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![](data/chem/img/SF4.gif)
![](data/chem/img/MG.gif)
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#11: Chemical | #12: Chemical | ChemComp-MG / | #13: Chemical | ChemComp-SF4 / | |
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-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: Mycobacterium tuberculosis WT RNAP transcription closed promoter complex with WhiB7 transcription factor Type: COMPLEX / Entity ID: #1-#10 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 66 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32712 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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