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- PDB-7um1: Structure of bacteriophage AR9 non-virion RNAP polymerase holoenz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7um1 | ||||||
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Title | Structure of bacteriophage AR9 non-virion RNAP polymerase holoenzyme determined by cryo-EM | ||||||
![]() | (DNA-directed RNA ...) x 5 | ||||||
![]() | TRANSCRIPTION / RNAP / deoxyuridine / template-strand promoter / sigma-like factor / gp226 | ||||||
Function / homology | ![]() DNA-directed RNA polymerase complex / RNA polymerase II activity / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
![]() | Leiman, P.G. / Fraser, A. / Sokolova, M.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase. Authors: Alec Fraser / Maria L Sokolova / Arina V Drobysheva / Julia V Gordeeva / Sergei Borukhov / John Jumper / Konstantin V Severinov / Petr G Leiman / ![]() ![]() ![]() Abstract: Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template ...Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 501.8 KB | Display | ![]() |
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PDB format | ![]() | 334.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 62.7 KB | Display | |
Data in CIF | ![]() | 97.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 24765MC ![]() 7s00C ![]() 7s01C ![]() 7um0C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-DNA-directed RNA ... , 5 types, 5 molecules AdcDC
#1: Protein | Mass: 54917.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Promoter-specificity subunit / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 51947.844 Da / Num. of mol.: 1 / Mutation: N-terminal His-tag Source method: isolated from a genetically manipulated source Details: N-terminal part of beta-prime subunit / Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 58112.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal part of beta subunit / Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 73100.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal part of beta-prime subunit / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A172JI62, DNA-directed RNA polymerase |
#5: Protein | Mass: 76978.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal part of beta subunit / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A172JHZ2, DNA-directed RNA polymerase |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/ZN.gif)
#6: Chemical | ChemComp-ZN / |
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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 |
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Sample preparation
Component | Name: Bacteriophage AR9 non-virion RNA polymerase holoenzyme Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 6.8 |
Specimen | Conc.: 20 mg/ml / 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 / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 43.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104471 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7S01 Accession code: 7S01 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.22 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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