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Yorodumi- PDB-7z8q: Cryo-EM structure of Mycobacterium tuberculosis RNA polymerase core -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z8q | ||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis RNA polymerase core | ||||||
Components | (DNA-directed RNA polymerase subunit ...Polymerase) x 4 | ||||||
Keywords | TRANSCRIPTION / RNA polymerase | ||||||
Function / homology | Function and homology information Antimicrobial action and antimicrobial resistance in Mtb / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / 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 ...Antimicrobial action and antimicrobial resistance in Mtb / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / 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 H37Rv (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.08 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 | 7z8q.cif.gz | 507.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z8q.ent.gz | 407.2 KB | Display | PDB format |
PDBx/mmJSON format | 7z8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/7z8q ftp://data.pdbj.org/pub/pdb/validation_reports/z8/7z8q | HTTPS FTP |
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-Related structure data
Related structure data | 14560MC 7q4uC 7q59C 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 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.: 1 Source method: isolated from a genetically manipulated source Details: L2E3G4C5 -> V Source: (gene. exp.) Mycobacterium tuberculosis 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.: 1 / Mutation: contains C-terminal 6xHis-tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoC, Rv0668, MTCI376.07c / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 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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-Non-polymers , 2 types, 3 molecules
#5: Chemical | #6: 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: DNA-dependent RNA polymerase core / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Molecular weight | Value: 0.4 MDa / Experimental value: NO |
Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 / Nominal defocus max: 7000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 49.6 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3064 |
-Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 721752 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55008 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7PP4 | ||||||||||||||||||||||||
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