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Yorodumi- PDB-7ogr: Structure of the apo-state of the bacteriophage PhiKZ non-virion ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ogr | |||||||||
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Title | Structure of the apo-state of the bacteriophage PhiKZ non-virion RNA polymerase | |||||||||
Components |
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Keywords | TRANSCRIPTION / RNA polymerase / PhiKZ / non-virion | |||||||||
Function / homology | PHIKZ123 / PHIKZ074 / PHIKZ068 / PHIKZ055 Function and homology information | |||||||||
Biological species | Pseudomonas phage phiKZ (virus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | de Martin Garrido, N. / Lai Wan Loong, Y.T.E. / Yakunina, M. / Aylett, C.H.S. | |||||||||
Funding support | United Kingdom, Russian Federation, 2items
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Citation | Journal: Nucleic Acids Res / Year: 2021 Title: Structure of the bacteriophage PhiKZ non-virion RNA polymerase. Authors: Natàlia deYMartín Garrido / Mariia Orekhova / Yuen Ting Emilie Lai Wan Loong / Anna Litvinova / Kailash Ramlaul / Tatyana Artamonova / Alexei S Melnikov / Pavel Serdobintsev / Christopher ...Authors: Natàlia deYMartín Garrido / Mariia Orekhova / Yuen Ting Emilie Lai Wan Loong / Anna Litvinova / Kailash Ramlaul / Tatyana Artamonova / Alexei S Melnikov / Pavel Serdobintsev / Christopher H S Aylett / Maria Yakunina / Abstract: Bacteriophage ΦKZ (PhiKZ) is the archetype of a family of massive bacterial viruses. It is considered to have therapeutic potential as its host, Pseudomonas aeruginosa, is an opportunistic, ...Bacteriophage ΦKZ (PhiKZ) is the archetype of a family of massive bacterial viruses. It is considered to have therapeutic potential as its host, Pseudomonas aeruginosa, is an opportunistic, intrinsically antibiotic resistant, pathogen that kills tens of thousands worldwide each year. ΦKZ is an incredibly interesting virus, expressing many systems that the host already possesses. On infection, it forms a 'nucleus', erecting a barrier around its genome to exclude host endonucleases and CRISPR-Cas systems. ΦKZ infection is independent of the host transcriptional apparatus. It expresses two different multi-subunit RNA polymerases (RNAPs): the virion RNAP (vRNAP) is injected with the viral DNA during infection to transcribe early genes, including those encoding the non-virion RNAP (nvRNAP), which transcribes all further genes. ΦKZ nvRNAP is formed by four polypeptides thought to represent homologues of the eubacterial β/β' subunits, and a fifth with unclear homology, but essential for transcription. We have resolved the structure of ΦKZ nvRNAP to better than 3.0 Å, shedding light on its assembly, homology, and the biological role of the fifth subunit: it is an embedded, integral member of the complex, the position, structural homology and biochemical role of which imply that it has evolved from an ancestral homologue to σ-factor. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ogr.cif.gz | 347.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ogr.ent.gz | 263.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ogr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ogr_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7ogr_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7ogr_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 7ogr_validation.cif.gz | 87.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/7ogr ftp://data.pdbj.org/pub/pdb/validation_reports/og/7ogr | HTTPS FTP |
-Related structure data
Related structure data | 12886MC 7ogpC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 5 molecules ABCDE
#2: Protein | Mass: 57976.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SDA7 |
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#3: Protein | Mass: 59419.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SD94 |
#4: Protein | Mass: 78780.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) / References: DNA-directed RNA polymerase |
#5: Protein | Mass: 77513.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SD88 |
#6: Protein | Mass: 62959.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SD39 |
-Protein/peptide / Non-polymers , 2 types, 2 molecules X
#1: Protein/peptide | Mass: 2741.370 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) |
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#7: Chemical | ChemComp-ZN / |
-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
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Molecular weight | Value: 0.3 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 Details: 15 mM Tris-Cl pH 8.0, 150 mM NaCl, 0.5 mM EDTA, 2 mM MgCl2, 1 mM DTT | |||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: 1-2 s blot |
-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 FIELD / Nominal magnification: 48000 X / Nominal defocus max: 3250 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 100 K |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 10582 / Details: TIFF movie mode |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 70 eV |
Image scans | Sampling size: 5 µm / Width: 5096 / Height: 4092 |
-Processing
EM software |
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Image processing | Details: Motion correction and dose-weighting in motioncor2 | ||||||||||||||||||||||||||||||||||||
CTF correction | Details: During reconstruction in RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3179799 Details: EMAN BATCHBOXER with low-pass butterworth preprocessing | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 855016 / Algorithm: FOURIER SPACE / Details: RELION 3.0 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER Details: Core conserved regions initially identified from comparison with PDB 6EDT - remainder built de novo | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6EDT Accession code: 6EDT / Source name: PDB / Type: experimental model |