[English] 日本語
Yorodumi- EMDB-4888: Structure of the core Vaccinia Virus DNA-dependent RNA polymerase... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4888 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the core Vaccinia Virus DNA-dependent RNA polymerase complex | ||||||||||||||||||||||||
Map data | Post-processed map used for building. | ||||||||||||||||||||||||
Sample |
| ||||||||||||||||||||||||
Keywords | Vaccinia / RNA polymerase / Transcription / Gene expression / VIRAL PROTEIN | ||||||||||||||||||||||||
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-binding transcription factor activity / DNA-templated transcription / DNA binding / zinc ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | Vaccinia virus GLV-1h68 | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||||||||||||||
Authors | Grimm C / Hillen HS | ||||||||||||||||||||||||
Funding support | Germany, 7 items
| ||||||||||||||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
-Validation report
Summary document | emd_4888_validation.pdf.gz | 982.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4888_full_validation.pdf.gz | 981.9 KB | Display | |
Data in XML | emd_4888_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_4888_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4888 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4888 | HTTPS FTP |
-Related structure data
Related structure data | 6ricMC 4889C 4890C 4891C 6ridC 6rieC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4888.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Post-processed map used for building. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.81 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Mask #4
+Additional map: Rap94 CTD focused 3D refinement half-map 1.
+Additional map: Rpo30 focused 3D refinement post-processed map.
+Additional map: Rap94 Domain2 focused 3D refinement map.
+Additional map: Rap94 CTD focused 3D refinement map.
+Additional map: Global 3D refinement map.
+Additional map: Composite map used for real space refinement.
+Additional map: Rap94 CTD focused 3D refinement half-map 1.
+Additional map: Rap94 Domain2 focused 3D refinement half-map 2.
+Additional map: Rap94 Domain2 focused 3D refinement half-map 1.
+Additional map: Rap94 Domain2 focused 3D refinement post-processed map.
+Additional map: Rap94 CTD focused 3D refinement post-processed map.
+Additional map: Rpo30 focused 3D refinement map.
+Additional map: Rpo30 focused 3D refinement half-map 1.
+Additional map: Rpo30 focused 3D refinement half-map 2.
+Half map: Global 3D refinement half-map 2.
+Half map: Global 3D refinement half-map 1.
-Sample components
+Entire : Core Vaccinia DNA-dependent RNA polymerase complex
+Supramolecule #1: Core Vaccinia DNA-dependent RNA polymerase complex
+Supramolecule #2: DNA-dependent RNA polymerase subunits
+Macromolecule #1: DNA-dependent RNA polymerase subunit rpo147
+Macromolecule #2: DNA-dependent RNA polymerase subunit rpo132
+Macromolecule #3: DNA-directed RNA polymerase 35 kDa subunit
+Macromolecule #4: DNA-directed RNA polymerase subunit
+Macromolecule #5: DNA-directed RNA polymerase 19 kDa subunit
+Macromolecule #6: DNA-dependent RNA polymerase subunit rpo18
+Macromolecule #7: RAP94 transcription factor
+Macromolecule #8: DNA-dependent RNA polymerase subunit rpo7
+Macromolecule #9: DNA-directed RNA polymerase 30 kDa polypeptide
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3609 / Average electron dose: 1.41 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / 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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
---|---|
Output model | PDB-6ric: |