+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3619 | |||||||||
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Title | RnQV1-W1118 empty capsid | |||||||||
Map data | Rosellinia necatrix quadrivirus 1 strain W1118 (RnQV1-1118), empty particle | |||||||||
Sample |
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Function / homology | Capsid protein / Capsid protein Function and homology information | |||||||||
Biological species | Rosellinia necatrix quadrivirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Mata CP / Luque D / Gomez-Blanco J / Rodriguez JM / Suzuki N / Ghabrial SA / Carrascosa JL / Trus BL / Caston JR | |||||||||
Citation | Journal: PLoS Pathog / Year: 2017 Title: Acquisition of functions on the outer capsid surface during evolution of double-stranded RNA fungal viruses. Authors: Carlos P Mata / Daniel Luque / Josué Gómez-Blanco / Javier M Rodríguez / José M González / Nobuhiro Suzuki / Said A Ghabrial / José L Carrascosa / Benes L Trus / José R Castón / Abstract: Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3. ...Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3.7 Å resolution of Rosellinia necatrix quadrivirus 1 (RnQV1), a fungal double-stranded (ds)RNA virus. RnQV1, the type species of the family Quadriviridae, has a multipartite genome consisting of four monocistronic segments. Whereas most dsRNA virus capsids are based on dimers of a single protein, the ~450-Å-diameter, T = 1 RnQV1 capsid is built of P2 and P4 protein heterodimers, each with more than 1000 residues. Despite a lack of sequence similarity between the two proteins, they have a similar α-helical domain, the structural signature shared with the lineage of the dsRNA bluetongue virus-like viruses. Domain insertions in P2 and P4 preferential sites provide additional functions at the capsid outer surface, probably related to enzyme activity. The P2 insertion has a fold similar to that of gelsolin and profilin, two actin-binding proteins with a function in cytoskeleton metabolism, whereas the P4 insertion suggests protease activity involved in cleavage of the P2 383-residue C-terminal region, absent in the mature viral particle. Our results indicate that the intimate virus-fungus partnership has altered the capsid genome-protective and/or receptor-binding functions. Fungal virus evolution has tended to allocate enzyme activities to the virus capsid outer surface. | |||||||||
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_3619.map.gz | 209.5 MB | EMDB map data format | |
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Header (meta data) | emd-3619-v30.xml emd-3619.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_3619.png | 277.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3619 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3619 | HTTPS FTP |
-Validation report
Summary document | emd_3619_validation.pdf.gz | 258.9 KB | Display | EMDB validaton report |
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Full document | emd_3619_full_validation.pdf.gz | 258 KB | Display | |
Data in XML | emd_3619_validation.xml.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3619 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3619 | HTTPS FTP |
-Related structure data
Related structure data | 5nd1MC 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_3619.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Rosellinia necatrix quadrivirus 1 strain W1118 (RnQV1-1118), empty particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 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
Entire | Name: Rosellinia necatrix quadrivirus 1 |
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Components |
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-Supramolecule #1: Rosellinia necatrix quadrivirus 1
Supramolecule | Name: Rosellinia necatrix quadrivirus 1 / type: virus / ID: 1 / Parent: 0 / 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 |
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Host (natural) | Organism: Rosellinia necatrix (fungus) |
Molecular weight | Experimental: 15.9 MDa |
Virus shell | Shell ID: 1 / Name: P2 and P4 / Diameter: 470.0 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | 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, 150 mM NaCl, 5 mM EDTA |
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Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Frames/image: 4-21 / Number real images: 1125 / Average electron dose: 1.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.5 µm / Calibrated defocus min: 0.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
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 | Protocol: BACKBONE TRACE |
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Output model | PDB-5nd1: |