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Yorodumi- PDB-7q4u: Cryo-EM structure of Mycobacterium tuberculosis RNA polymerase ho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q4u | ||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis RNA polymerase holoenzyme octamer comprising sigma factor SigB | ||||||
Components |
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Keywords | TRANSCRIPTION / DNA-dependent RNA polymerase / alternative sigma | ||||||
Function / homology | Function and homology information RNA polymerase core enzyme binding / 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 / response to heat ...RNA polymerase core enzyme binding / 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 / response to heat / response to hypoxia / protein dimerization activity / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / positive regulation of 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: 4.39 Å | ||||||
Authors | Brodolin, K. | ||||||
Funding support | France, 1items
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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: Morichaud, Z. / Trapani, S. / Vishwakarma, R.K. / Chaloin, L. / Lionne, C. / Lai-Kee-Him, J. / Bron, P. / Brodolin, K. #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 | 7q4u.cif.gz | 4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7q4u.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/7q4u ftp://data.pdbj.org/pub/pdb/validation_reports/q4/7q4u | HTTPS FTP |
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-Related structure data
Related structure data | 13817MC 7q59C 7z8qC 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, 40 molecules ABGHMNSTZAAFAGALAMARASACIOVBAHANATADJPWCAIA...
#1: Protein | Mass: 37745.328 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoA, Rv3457c, MTCY13E12.10c / Plasmid: pMR4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WGZ1, DNA-directed RNA polymerase #2: Protein | Mass: 129602.344 Da / Num. of mol.: 8 / Mutation: L2E3G4C5 -> V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoB, Rv0667, MTCI376.08c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WGY9, DNA-directed RNA polymerase #3: Protein | Mass: 147438.344 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoC, Rv0668, MTCI376.07c / Plasmid: pMR4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WGY7, DNA-directed RNA polymerase #4: Protein | Mass: 11851.140 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoZ, Rv1390, MTCY21B4.07 / Plasmid: pMR4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WGY5, DNA-directed RNA polymerase |
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-Protein , 1 types, 8 molecules FLRYEAKAQAWA
#5: Protein | Mass: 38572.773 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: sigB, mysB, Rv2710 / Plasmid: pET28a / Details (production host): derivative containing Rv2710 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WGI5 |
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-Non-polymers , 2 types, 24 molecules
#6: Chemical | ChemComp-ZN / #7: Chemical | ChemComp-MG / |
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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 |
-Sample preparation
Component | Name: RNA polymerase holoenzyme with sigma factor sigB / Type: COMPLEX Details: RNA polymerase holoenzyme assembled from individually expressed RNA polymerase core and sigma factor sigB Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Value: 3.2 MDa / Experimental value: NO |
Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pMR4, pET28a |
Buffer solution | pH: 7.9 |
Specimen | Conc.: 1.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | 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 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 254380 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D4 (2x4 fold dihedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115457 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7PP4 |