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Yorodumi- PDB-5nd1: Viral evolution results in multiple, surface-allocated enzymatic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nd1 | |||||||||
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Title | Viral evolution results in multiple, surface-allocated enzymatic activities in a fungal double-stranded RNA virus | |||||||||
Components | (Capsid protein) x 2 | |||||||||
Keywords | VIRUS / RnQV1 / dsRNA virus / fungal virus | |||||||||
Function / homology | Capsid protein / Capsid protein Function and homology information | |||||||||
Biological species | Rosellinia necatrix quadrivirus 1 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Mata, C.P. / Luque, D. / Gomez Blanco, J. / Rodriguez, J.M. / Suzuki, N. / Ghabrial, S.A. / Carrascosa, J.L. / Trus, B.L. / Caston, J.R. | |||||||||
Funding support | Spain, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5nd1.cif.gz | 353.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nd1.ent.gz | 266.7 KB | Display | PDB format |
PDBx/mmJSON format | 5nd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nd1_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5nd1_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5nd1_validation.xml.gz | 97.2 KB | Display | |
Data in CIF | 5nd1_validation.cif.gz | 134 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/5nd1 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5nd1 | HTTPS FTP |
-Related structure data
Related structure data | 3619MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 147782.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rosellinia necatrix quadrivirus 1 / References: UniProt: M1VMJ0 |
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#2: Protein | Mass: 113439.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rosellinia necatrix quadrivirus 1 / References: UniProt: M1VHN2 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: virus / Type: VIRUS / Entity ID: all |
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Molecular weight | Value: 15.9 MDa / Experimental value: YES |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Rosellinia necatrix |
Virus shell | Name: P2 and P4 capsid proteins / Diameter: 470 nm / Triangulation number (T number): 1 |
Buffer solution | pH: 7.8 / Details: 50 mM Tris-HCl pH 7.8, 150 mM NaCl, 5 mM EDTA |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: LEICA EM CPC / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated defocus min: 700 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 1.7 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Movie frames/image: 24 / Used frames/image: 4-21 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 53683 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37531 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE |