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Yorodumi- EMDB-4891: Structural basis of Poxvirus transcription: transcribing and capp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4891 | ||||||||||||||||||||||||
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Title | Structural basis of Poxvirus transcription: transcribing and capping complexes (nucleic acid free particle population) | ||||||||||||||||||||||||
Map data | Post-processed map. | ||||||||||||||||||||||||
Sample |
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Biological species | Vaccinia virus | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||||||||||||||
Authors | Hillen HS / Bartuli J / Grimm C / Dienemann C / Bedenk K / Szalay A / Fischer U / Cramer P | ||||||||||||||||||||||||
Funding support | Germany, 7 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4891.map.gz | 10.3 MB | EMDB map data format | |
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Header (meta data) | emd-4891-v30.xml emd-4891.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4891_fsc.xml | 12.1 KB | Display | FSC data file |
Images | emd_4891.png | 114.1 KB | ||
Masks | emd_4891_msk_1.map | 149.9 MB | Mask map | |
Others | emd_4891_additional.map.gz emd_4891_additional_1.map.gz emd_4891_half_map_1.map.gz emd_4891_half_map_2.map.gz | 117.8 MB 117.8 MB 118.5 MB 118.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4891 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4891 | HTTPS FTP |
-Validation report
Summary document | emd_4891_validation.pdf.gz | 450.8 KB | Display | EMDB validaton report |
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Full document | emd_4891_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | emd_4891_validation.xml.gz | 18.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4891 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4891 | HTTPS FTP |
-Related structure data
Related structure data | 4888C 4889C 4890C 6ricC 6ridC 6rieC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4891.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Post-processed map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_4891_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: 3D Refinement map.
File | emd_4891_additional.map | ||||||||||||
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Annotation | 3D Refinement map. | ||||||||||||
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Density Histograms |
-Additional map: 3D Refinement map.
File | emd_4891_additional_1.map | ||||||||||||
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Annotation | 3D Refinement map. | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_4891_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_4891_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional ca...
Entire | Name: Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional capping complex |
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Components |
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-Supramolecule #1: Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional ca...
Supramolecule | Name: Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional capping complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 |
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Source (natural) | Organism: Vaccinia virus / Strain: 1h68 |
Recombinant expression | Organism: Vaccinia virus / Recombinant strain: 1h439 |
Molecular weight | Theoretical: 580 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4958 / Average electron dose: 1.02 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |