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Yorodumi- PDB-8p0n: Cryo EM map and model of the vaccinia RNA polymerase intermediate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p0n | ||||||
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Title | Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex shallow conformation | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA polymerase / RNAP / Vaccinia / MPox / PIC / pre-initiation complex | ||||||
Function / homology | Function and homology information inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / viral transcription / DNA-directed RNA polymerase complex / virion component / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity ...inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / viral transcription / DNA-directed RNA polymerase complex / virion component / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / DNA-templated transcription / GTP binding / DNA binding / RNA binding / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Vaccinia virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å | ||||||
Authors | Grimm, C. / Jungwirth, S. / Fischer, U. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex (CASP target) Authors: Grimm, C. / Jungwirth, S. / Fischer, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p0n.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8p0n.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8p0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/8p0n ftp://data.pdbj.org/pub/pdb/validation_reports/p0/8p0n | HTTPS FTP |
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-Related structure data
Related structure data | 17336MC 8p0jC 8p0kC 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 ... , 8 types, 8 molecules ABCEFGJS
#1: Protein | Mass: 146995.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG105, RPO147, J6R / Production host: Vaccinia virus / References: UniProt: P20504, DNA-directed RNA polymerase |
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#2: Protein | Mass: 133526.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG151, RPO132, A24R / Production host: Vaccinia virus / References: UniProt: P68694, DNA-directed RNA polymerase |
#3: Protein | Mass: 35430.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG156, RPO35, A29L / Production host: Vaccinia virus / References: UniProt: P21087, DNA-directed RNA polymerase |
#4: Protein | Mass: 21365.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG103, RPO22, J4R / Production host: Vaccinia virus / References: UniProt: P68608, DNA-directed RNA polymerase |
#5: Protein | Mass: 19020.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG131, RPO19, A5R / Production host: Vaccinia virus / References: UniProt: P68610, DNA-directed RNA polymerase |
#6: Protein | Mass: 17917.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG119, RPO18, D7R / Production host: Vaccinia virus / References: UniProt: P21034, DNA-directed RNA polymerase |
#9: Protein | Mass: 7299.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG090, RPO7, G5.5R / Production host: Vaccinia virus / References: UniProt: P68315, DNA-directed RNA polymerase |
#13: Protein | Mass: 29834.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG066, RPO30, E4L / Production host: Vaccinia virus / References: UniProt: P21082, DNA-directed RNA polymerase |
-Intermediate transcription factor 3 ... , 2 types, 2 molecules HI
#7: Protein | Mass: 44662.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG150, VITF3L, A23R / Production host: Vaccinia virus / References: UniProt: P20998 |
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#8: Protein | Mass: 33618.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG134, VITF3S, A8R / Production host: synthetic construct (others) / References: UniProt: P20986 |
-MRNA-capping enzyme ... , 2 types, 2 molecules LO
#10: Protein | Mass: 33396.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG124, D12L / Production host: Vaccinia virus / References: UniProt: P20980 |
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#12: Protein | Mass: 96888.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: OPG113, D1R / Production host: Vaccinia virus References: UniProt: P20979, mRNA 5'-phosphatase, mRNA guanylyltransferase, mRNA (guanine-N7)-methyltransferase |
-DNA chain , 2 types, 2 molecules NT
#11: DNA chain | Mass: 21587.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Production host: synthetic construct (others) |
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#14: DNA chain | Mass: 21675.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Production host: synthetic construct (others) |
-Non-polymers , 2 types, 5 molecules
#15: Chemical | ChemComp-MG / |
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#16: 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
Component | Name: Vaccinia DNA-directed RNA polymerase open promoter intermediate pre-initiation complex Type: COMPLEX / Entity ID: #1-#7, #9-#13, #8, #14 / Source: NATURAL |
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Molecular weight | Value: 0.75 MDa / Experimental value: YES |
Source (natural) | Organism: Vaccinia virus |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: 2200 nm / Nominal defocus min: 1200 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 70 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_4746: / 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: 9318600 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1395666 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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