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Yorodumi- PDB-7zf2: Protomeric substructure from an octameric assembly of M. tubercul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zf2 | ||||||||||||
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Title | Protomeric substructure from an octameric assembly of M. tuberculosis RNA polymerase in complex with sigma-b initiation factor | ||||||||||||
Components |
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Keywords | TRANSCRIPTION / RNA polymerase / self-assembly / octamer / tuberculosis / stress response / hibernation | ||||||||||||
Function / homology | Function and homology information Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / 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 ...Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / 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 / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å | ||||||||||||
Authors | Trapani, S. / Bron, P. / Lai Kee Him, J. / Brodolin, K. / Morichaud, Z. / Vishwakarma, R. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization. Authors: Zakia Morichaud / Stefano Trapani / Rishi K Vishwakarma / Laurent Chaloin / Corinne Lionne / Joséphine Lai-Kee-Him / Patrick Bron / Konstantin Brodolin / Abstract: Self-assembly of macromolecules into higher-order symmetric structures is fundamental for the regulation of biological processes. Higher-order symmetric structure self-assembly by the gene expression ...Self-assembly of macromolecules into higher-order symmetric structures is fundamental for the regulation of biological processes. Higher-order symmetric structure self-assembly by the gene expression machinery, such as bacterial DNA-dependent RNA polymerase (RNAP), has never been reported before. Here, we show that the stress-response σ factor from the human pathogen, Mycobacterium tuberculosis, induces the RNAP holoenzyme oligomerization into a supramolecular complex composed of eight RNAP units. Cryo-electron microscopy revealed a pseudo-symmetric structure of the RNAP octamer in which RNAP protomers are captured in an auto-inhibited state and display an open-clamp conformation. The structure shows that σ is sequestered by the RNAP flap and clamp domains. The transcriptional activator RbpA prevented octamer formation by promoting the initiation-competent RNAP conformation. Our results reveal that a non-conserved region of σ is an allosteric controller of transcription initiation and demonstrate how basal transcription factors can regulate gene expression by modulating the RNAP holoenzyme assembly and hibernation. #1: Journal: Biorxiv / Year: 2022 Title: Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization Authors: Morichaud, Z. / Trapani, S. / Vishwakarma, R. / Chaloin, L. / Lionne, C. / Lai-Kee-Him, J. / Bron, P. / Brodolin, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zf2.cif.gz | 555 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zf2.ent.gz | 435.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/7zf2 ftp://data.pdbj.org/pub/pdb/validation_reports/zf/7zf2 | HTTPS FTP |
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-Related structure data
Related structure data | 14696MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: rpoA, MT3564 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGZ0, DNA-directed RNA polymerase #2: Protein | | Mass: 129602.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: rpoB, MT0695 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGY8, DNA-directed RNA polymerase #3: Protein | | Mass: 147438.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: rpoC, Rv0668, MTCI376.07c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGY7, DNA-directed RNA polymerase #4: Protein | | Mass: 11851.140 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: rpoZ, MT1435 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGY4, DNA-directed RNA polymerase |
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-Protein , 1 types, 1 molecules F
#5: Protein | Mass: 38572.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: sigB, mysB, MT2783 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGI4 |
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-Non-polymers , 2 types, 3 molecules
#6: Chemical | #7: Chemical | ChemComp-MG / | |
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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: M. tuberculosis RNA polymerase in complex with sigma-b initiation factor Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.101 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.21 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K |
-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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 7000 nm / Nominal defocus min: 500 nm |
Image recording | Average exposure time: 8 sec. / Electron dose: 49.6 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3064 |
Image scans | Movie frames/image: 31 |
-Processing
EM software |
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Image processing | Details: Movie frames were aligned, dose-weighted, binned by two and averaged using Motioncor2 (Zheng S.Q Nat. Methods. 2017; 14: 331-332). Movie sums were used for contrast transfer function (CTF) ...Details: Movie frames were aligned, dose-weighted, binned by two and averaged using Motioncor2 (Zheng S.Q Nat. Methods. 2017; 14: 331-332). Movie sums were used for contrast transfer function (CTF) estimation with Gctf (Zhang K. J. Struct. Biol. 2016; 193: 1-12) | ||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267457 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |