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- PDB-6rfl: Structure of the complete Vaccinia DNA-dependent RNA polymerase c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rfl | |||||||||
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Title | Structure of the complete Vaccinia DNA-dependent RNA polymerase complex | |||||||||
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![]() | VIRAL PROTEIN / Vaccinia / RNA polymerase / RNA Polymerase complex / RNAP / vRNAP / complete vRNAP | |||||||||
Function / homology | ![]() polynucleotide 5'-phosphatase / virion component => GO:0044423 / polynucleotide 5'-phosphatase activity / viral transcription / ribonucleoside triphosphate phosphatase activity / DNA-templated transcription termination / DNA-directed RNA polymerase activity / ribonucleoside binding / virion component / DNA-directed RNA polymerase ...polynucleotide 5'-phosphatase / virion component => GO:0044423 / polynucleotide 5'-phosphatase activity / viral transcription / ribonucleoside triphosphate phosphatase activity / DNA-templated transcription termination / DNA-directed RNA polymerase activity / ribonucleoside binding / virion component / DNA-directed RNA polymerase / mRNA guanylyltransferase activity / nucleoside-triphosphate phosphatase / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å | |||||||||
![]() | Grimm, C. / Hillen, S.H. / Bedenk, K. / Bartuli, J. / Neyer, S. / Zhang, Q. / Huettenhofer, A. / Erlacher, M. / Dienemann, C. / Schlosser, A. ...Grimm, C. / Hillen, S.H. / Bedenk, K. / Bartuli, J. / Neyer, S. / Zhang, Q. / Huettenhofer, A. / Erlacher, M. / Dienemann, C. / Schlosser, A. / Urlaub, H. / Boettcher, B. / Szalay, A.A. / Cramer, P. / Fischer, U. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of Poxvirus Transcription: Vaccinia RNA Polymerase Complexes. Authors: Clemens Grimm / Hauke S Hillen / Kristina Bedenk / Julia Bartuli / Simon Neyer / Qian Zhang / Alexander Hüttenhofer / Matthias Erlacher / Christian Dienemann / Andreas Schlosser / Henning ...Authors: Clemens Grimm / Hauke S Hillen / Kristina Bedenk / Julia Bartuli / Simon Neyer / Qian Zhang / Alexander Hüttenhofer / Matthias Erlacher / Christian Dienemann / Andreas Schlosser / Henning Urlaub / Bettina Böttcher / Aladar A Szalay / Patrick Cramer / Utz Fischer / ![]() ![]() ![]() Abstract: Poxviruses encode a multisubunit DNA-dependent RNA polymerase (vRNAP) that carries out viral gene expression in the host cytoplasm. We report cryo-EM structures of core and complete vRNAP enzymes ...Poxviruses encode a multisubunit DNA-dependent RNA polymerase (vRNAP) that carries out viral gene expression in the host cytoplasm. We report cryo-EM structures of core and complete vRNAP enzymes from Vaccinia virus at 2.8 Å resolution. The vRNAP core enzyme resembles eukaryotic RNA polymerase II (Pol II) but also reveals many virus-specific features, including the transcription factor Rap94. The complete enzyme additionally contains the transcription factor VETF, the mRNA processing factors VTF/CE and NPH-I, the viral core protein E11, and host tRNA. This complex can carry out the entire early transcription cycle. The structures show that Rap94 partially resembles the Pol II initiation factor TFIIB, that the vRNAP subunit Rpo30 resembles the Pol II elongation factor TFIIS, and that NPH-I resembles chromatin remodeling enzymes. Together with the accompanying paper (Hillen et al., 2019), these results provide the basis for unraveling the mechanisms of poxvirus transcription and RNA processing. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 955.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 896.3 KB | Display | ![]() |
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Full document | ![]() | 953.5 KB | Display | |
Data in XML | ![]() | 155.8 KB | Display | |
Data in CIF | ![]() | 249.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4868MC ![]() 6rfgC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA-dependent RNA polymerase subunit ... , 4 types, 4 molecules BGJA
#1: Protein | Mass: 133526.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#4: Protein | Mass: 17917.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#6: Protein | Mass: 7299.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#12: Protein | Mass: 146995.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-DNA-directed RNA polymerase ... , 4 types, 4 molecules EFCS
#2: Protein | Mass: 21365.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Protein | Mass: 19020.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#14: Protein | Mass: 35430.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#15: Protein | Mass: 30074.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein , 6 types, 7 molecules ILORQKY
#5: Protein | Mass: 93667.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: H4L, List098, LIVPclone14_110, VAC_DPP10_113, VAC_DPP11_113, VAC_DPP12_113, VAC_DPP13_113, VAC_DPP15_113, VAC_DPP16_113, VAC_DPP17_113, VAC_DPP19_113, VAC_DPP20_113, VAC_DPP21_113, VAC_DPP9_ ...Gene: H4L, List098, LIVPclone14_110, VAC_DPP10_113, VAC_DPP11_113, VAC_DPP12_113, VAC_DPP13_113, VAC_DPP15_113, VAC_DPP16_113, VAC_DPP17_113, VAC_DPP19_113, VAC_DPP20_113, VAC_DPP21_113, VAC_DPP9_113, VACAC2_113, VACCL3_113, VACV_098, VACV_TT9_123 Production host: ![]() References: UniProt: Q1PIU7, UniProt: B9U1I7*PLUS, DNA-directed RNA polymerase | ||||
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#7: Protein | Mass: 33396.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: B9U1L2, mRNA (guanine-N7)-methyltransferase | ||||
#8: Protein | Mass: 96888.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
#9: Protein | Mass: 14914.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #10: Protein | | Mass: 82398.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #13: Protein | | Mass: 72465.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: B9U1K8, nucleoside-triphosphate phosphatase |
-RNA chain , 1 types, 1 molecules U
#11: RNA chain | Mass: 23108.650 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 3 types, 66 molecules 




#16: Chemical | ChemComp-ZN / #17: Chemical | ChemComp-MG / | #18: Water | ChemComp-HOH / | |
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-Details
Has protein modification | 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 |
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Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Conc.: 0.1 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 |
Image recording | Electron dose: 50 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.15.1_3469: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 618338 / Symmetry type: POINT |