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Yorodumi- EMDB-3438: Three-dimensional reconstruction of W1118 strain Rosellinia necat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3438 | |||||||||
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Title | Three-dimensional reconstruction of W1118 strain Rosellinia necatrix quadrivirus 1 | |||||||||
Map data | Reconstruction of Rosellinia necatrix quadrivirus 1 strain W1075 | |||||||||
Sample |
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Keywords | dsRNA virus / quadrivirus / 3DR / fungal virus | |||||||||
Biological species | Rosellinia necatrix quadrivirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 9.1 Å | |||||||||
Authors | Luque D / Mata CP / Gonzalez-Camacho F / Gonzalez JM / Gomez-Blanco J / Alfonso C / Rivas G / Havens WM / Kanematsu S / Suzuki N ...Luque D / Mata CP / Gonzalez-Camacho F / Gonzalez JM / Gomez-Blanco J / Alfonso C / Rivas G / Havens WM / Kanematsu S / Suzuki N / Ghabrial SA / Trus BL / Caston JR | |||||||||
Citation | Journal: J Virol / Year: 2016 Title: Heterodimers as the Structural Unit of the T=1 Capsid of the Fungal Double-Stranded RNA Rosellinia necatrix Quadrivirus 1. Authors: Daniel Luque / Carlos P Mata / Fernando González-Camacho / José M González / Josué Gómez-Blanco / Carlos Alfonso / Germán Rivas / Wendy M Havens / Satoko Kanematsu / Nobuhiro Suzuki / ...Authors: Daniel Luque / Carlos P Mata / Fernando González-Camacho / José M González / Josué Gómez-Blanco / Carlos Alfonso / Germán Rivas / Wendy M Havens / Satoko Kanematsu / Nobuhiro Suzuki / Said A Ghabrial / Benes L Trus / José R Castón / Abstract: Most double-stranded RNA (dsRNA) viruses are transcribed and replicated in a specialized icosahedral capsid with a T=1 lattice consisting of 60 asymmetric capsid protein (CP) dimers. These capsids ...Most double-stranded RNA (dsRNA) viruses are transcribed and replicated in a specialized icosahedral capsid with a T=1 lattice consisting of 60 asymmetric capsid protein (CP) dimers. These capsids help to organize the viral genome and replicative complex(es). They also act as molecular sieves that isolate the virus genome from host defense mechanisms and allow the passage of nucleotides and viral transcripts. Rosellinia necatrix quadrivirus 1 (RnQV1), the type species of the family Quadriviridae, is a dsRNA fungal virus with a multipartite genome consisting of four monocistronic segments (segments 1 to 4). dsRNA-2 and dsRNA-4 encode two CPs (P2 and P4, respectively), which coassemble into ∼450-Å-diameter capsids. We used three-dimensional cryo-electron microscopy combined with complementary biophysical techniques to determine the structures of RnQV1 virion strains W1075 and W1118. RnQV1 has a quadripartite genome, and the capsid is based on a single-shelled T=1 lattice built of P2-P4 dimers. Whereas the RnQV1-W1118 capsid is built of full-length CP, P2 and P4 of RnQV1-W1075 are cleaved into several polypeptides, maintaining the capsid structural organization. RnQV1 heterodimers have a quaternary organization similar to that of homodimers of reoviruses and other dsRNA mycoviruses. The RnQV1 capsid is the first T=1 capsid with a heterodimer as an asymmetric unit reported to date and follows the architectural principle for dsRNA viruses that a 120-subunit capsid is a conserved assembly that supports dsRNA replication and organization. IMPORTANCE: Given their importance to health, members of the family Reoviridae are the basis of most structural and functional studies and provide much of our knowledge of dsRNA viruses. Analysis of ...IMPORTANCE: Given their importance to health, members of the family Reoviridae are the basis of most structural and functional studies and provide much of our knowledge of dsRNA viruses. Analysis of bacterial, protozoal, and fungal dsRNA viruses has improved our understanding of their structure, function, and evolution, as well. Here, we studied a dsRNA virus that infects the fungus Rosellinia necatrix, an ascomycete that is pathogenic to a wide range of plants. Using three-dimensional cryo-electron microscopy and analytical ultracentrifugation analysis, we determined the structure and stoichiometry of Rosellinia necatrix quadrivirus 1 (RnQV1). The RnQV1 capsid is a T=1 capsid with 60 heterodimers as the asymmetric units. The large amount of genetic information used by RnQV1 to construct a simple T=1 capsid is probably related to the numerous virus-host and virus-virus interactions that it must face in its life cycle, which lacks an extracellular phase. | |||||||||
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_3438.map.gz | 44.3 MB | EMDB map data format | |
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Header (meta data) | emd-3438-v30.xml emd-3438.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_3438.jpg | 115.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3438 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3438 | HTTPS FTP |
-Validation report
Summary document | emd_3438_validation.pdf.gz | 307.5 KB | Display | EMDB validaton report |
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Full document | emd_3438_full_validation.pdf.gz | 306.6 KB | Display | |
Data in XML | emd_3438_validation.xml.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3438 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3438 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3438.map.gz / Format: CCP4 / Size: 46.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Rosellinia necatrix quadrivirus 1 strain W1075 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Rosellinia necatrix quadrivirus 1 empty particles W1118 strain
Entire | Name: Rosellinia necatrix quadrivirus 1 empty particles W1118 strain |
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Components |
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-Supramolecule #1000: Rosellinia necatrix quadrivirus 1 empty particles W1118 strain
Supramolecule | Name: Rosellinia necatrix quadrivirus 1 empty particles W1118 strain type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1 |
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Molecular weight | Experimental: 15.9 MDa / Theoretical: 15.6 MDa / Method: Sedimentation |
-Supramolecule #1: Rosellinia necatrix quadrivirus 1
Supramolecule | Name: Rosellinia necatrix quadrivirus 1 / type: virus / ID: 1 / Name.synonym: RnQV1 / NCBI-ID: 1000373 / Sci species name: Rosellinia necatrix quadrivirus 1 / Sci species strain: W1118 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: RnQV1 |
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Host (natural) | Organism: Rosellinia necatrix (fungus) / Strain: W1118 / synonym: FUNGI |
Molecular weight | Experimental: 15.9 MDa / Theoretical: 15.6 MDa |
Virus shell | Shell ID: 1 / Diameter: 470 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 / Details: 50 mM Tris-HCl pH 7.8, 5 mM EDTA, 150 mM NaCl |
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Staining | Type: NEGATIVE Details: Samples were applied to grids, blotted and plunged into liquid ethane |
Grid | Details: R 2/2 Quantifoil grids |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Feb 18, 2014 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 324 / Average electron dose: 10 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Phase flipping & amplitude decay |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: OTHER / Software - Name: Xmipp / Number images used: 23926 |