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Yorodumi- PDB-6rid: Structure of Vaccinia Virus DNA-dependent RNA polymerase elongati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rid | ||||||||||||||||||||||||
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Title | Structure of Vaccinia Virus DNA-dependent RNA polymerase elongation complex | ||||||||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / Vaccinia / RNA polymerase / Transcription / Gene expression | ||||||||||||||||||||||||
Function / homology | Function and homology information virion component => GO:0044423 / viral transcription / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding / zinc ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | Vaccinia virus GLV-1h68 Vaccinia virus | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||||||||
Authors | Hillen, H.S. / Bartuli, J. / Grimm, C. / Dienemann, C. / Bedenk, K. / Szalar, A. / Fischer, U. / Cramer, P. | ||||||||||||||||||||||||
Funding support | Germany, 7items
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Citation | Journal: Cell / Year: 2019 Title: Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes. Authors: Hauke S Hillen / Julia Bartuli / Clemens Grimm / Christian Dienemann / Kristina Bedenk / Aladar A Szalay / Utz Fischer / Patrick Cramer / Abstract: Poxviruses use virus-encoded multisubunit RNA polymerases (vRNAPs) and RNA-processing factors to generate mG-capped mRNAs in the host cytoplasm. In the accompanying paper, we report structures of ...Poxviruses use virus-encoded multisubunit RNA polymerases (vRNAPs) and RNA-processing factors to generate mG-capped mRNAs in the host cytoplasm. In the accompanying paper, we report structures of core and complete vRNAP complexes of the prototypic Vaccinia poxvirus (Grimm et al., 2019; in this issue of Cell). Here, we present the cryo-electron microscopy (cryo-EM) structures of Vaccinia vRNAP in the form of a transcribing elongation complex and in the form of a co-transcriptional capping complex that contains the viral capping enzyme (CE). The trifunctional CE forms two mobile modules that bind the polymerase surface around the RNA exit tunnel. RNA extends from the vRNAP active site through this tunnel and into the active site of the CE triphosphatase. Structural comparisons suggest that growing RNA triggers large-scale rearrangements on the surface of the transcription machinery during the transition from transcription initiation to RNA capping and elongation. Our structures unravel the basis for synthesis and co-transcriptional modification of poxvirus RNA. | ||||||||||||||||||||||||
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 | 6rid.cif.gz | 602 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rid.ent.gz | 490.5 KB | Display | PDB format |
PDBx/mmJSON format | 6rid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/6rid ftp://data.pdbj.org/pub/pdb/validation_reports/ri/6rid | HTTPS FTP |
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-Related structure data
Related structure data | 4889MC 4888C 4890C 4891C 6ricC 6rieC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-dependent RNA polymerase subunit ... , 4 types, 4 molecules ABGJ
#1: Protein | Mass: 146995.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus GLV-1h68 / Gene: GL125 / Production host: Vaccinia virus / Variant (production host): 1h439 / References: UniProt: B9U1I2, 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 GLV-1h68 / Gene: GL194 / Production host: Vaccinia virus / Variant (production host): 1h439 / References: UniProt: B9U1Q1, 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 GLV-1h68 / Gene: GL147 / Production host: Vaccinia virus / Variant (production host): 1h439 / References: UniProt: B9U1K4, DNA-directed RNA polymerase |
#7: Protein | Mass: 7299.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus GLV-1h68 / Gene: GL107 / Production host: Vaccinia virus / Variant (production host): 1h439 / References: UniProt: B9U1G3, DNA-directed RNA polymerase |
-DNA-directed RNA polymerase ... , 4 types, 4 molecules CEFS
#3: Protein | Mass: 35430.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus GLV-1h68 / Gene: GL205 / Production host: Vaccinia virus / Variant (production host): 1h439 / References: UniProt: B9U1R2, DNA-directed RNA polymerase |
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#4: Protein | Mass: 21365.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus GLV-1h68 / Gene: GL123 / Production host: Vaccinia virus / Variant (production host): 1h439 / References: UniProt: B9U1I0, 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 GLV-1h68 / Gene: GL167 / Production host: Vaccinia virus / Variant (production host): 1h439 / References: UniProt: B9U1M4, DNA-directed RNA polymerase |
#8: Protein | Mass: 29834.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus GLV-1h68 / Gene: GL076 / Production host: Vaccinia virus / Variant (production host): 1h439 / References: UniProt: B9U1D1, DNA-directed RNA polymerase |
-DNA chain , 2 types, 2 molecules NT
#9: DNA chain | Mass: 14775.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vaccinia virus |
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#10: DNA chain | Mass: 14786.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vaccinia virus |
-RNA chain , 1 types, 1 molecules P
#11: RNA chain | Mass: 9742.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vaccinia virus |
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-Non-polymers , 2 types, 5 molecules
#12: Chemical | ChemComp-MG / |
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#13: Chemical | ChemComp-ZN / |
-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 |
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Molecular weight | Value: 0.45 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.02 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4958 |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / 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: 632458 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110733 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |