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Yorodumi- EMDB-6322: Genome and RdRp structure within the capsid of no-transcribing cy... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6322 | |||||||||
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Title | Genome and RdRp structure within the capsid of no-transcribing cypovirus | |||||||||
Map data | Genome and RdRp structures of non-transcribing cypovirus imposed D3 symmetry | |||||||||
Sample |
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Keywords | non-transcribing cypovirus / RNA-dependent RNA polymerase / genome structure / dsRNA virus | |||||||||
Function / homology | RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / viral genome replication / RNA-dependent RNA polymerase activity / RNA binding / RNA-dependent RNA polymerase Function and homology information | |||||||||
Biological species | Bombyx mori cypovirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Liu H / Cheng L | |||||||||
Citation | Journal: Science / Year: 2015 Title: Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus. Authors: Hongrong Liu / Lingpeng Cheng / Abstract: Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps ...Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps within the capsids have been unknown. Here we report the structures of RdRps and associated RNAs within nontranscribing and transcribing cypoviruses (NCPV and TCPV, respectively), using a combination of cryo-electron microscopy (cryo-EM) and a symmetry-mismatch reconstruction method. The RdRps and associated RNAs appear to exhibit a pseudo-D3 symmetric organization in both NCPV and TCPV. However, the molecular interactions between RdRps and the genomic RNA were found to differ in these states. Our work provides insight into the mechanisms of the replication and transcription in dsRNA viruses and paves a way for structural determination of lower-symmetry complexes enclosed in higher-symmetry structures. | |||||||||
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_6322.map.gz | 93.1 MB | EMDB map data format | |
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Header (meta data) | emd-6322-v30.xml emd-6322.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_6322.jpg | 256.9 KB | ||
Masks | emd_6322_msk_1.map emd_6322_msk_2.map | 2.8 MB 19.5 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6322 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6322 | HTTPS FTP |
-Validation report
Summary document | emd_6322_validation.pdf.gz | 406.8 KB | Display | EMDB validaton report |
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Full document | emd_6322_full_validation.pdf.gz | 406.4 KB | Display | |
Data in XML | emd_6322_validation.xml.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6322 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6322 | HTTPS FTP |
-Related structure data
Related structure data | 3ja5MC 6321C 3ja4C M: atomic model generated by this map 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_6322.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Genome and RdRp structures of non-transcribing cypovirus imposed D3 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.392 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Segmentation: structure of the masked RdRp at ~4.8 angstrom...
Annotation | structure of the masked RdRp at ~4.8 angstrom resolution (with D3 symmetry imposed) | ||||||||||||
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File | emd_6322_msk_1.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Segmentation: a RdRp complexe under a fivefold turret at...
Annotation | a RdRp complexe under a fivefold turret at ~6 angstrom resolution (masked from the full density map with D3 symmetry imposed) | ||||||||||||
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File | emd_6322_msk_2.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : non-transcribing cypovirus
Entire | Name: non-transcribing cypovirus |
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Components |
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-Supramolecule #1000: non-transcribing cypovirus
Supramolecule | Name: non-transcribing cypovirus / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Bombyx mori cypovirus 1
Supramolecule | Name: Bombyx mori cypovirus 1 / type: virus / ID: 1 / NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 715 Å |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Apr 10, 2010 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 125390 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 75000 |
Sample stage | Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Symmetry-mismatch reconstruction of icosahedral with D3 symmetry imposed |
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CTF correction | Details: Each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Software - Name: MRC / Number images used: 28000 |