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Yorodumi- PDB-3iym: Backbone Trace of the Capsid Protein Dimer of a Fungal Partitivir... -
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-Basic information
Entry | Database: PDB / ID: 3iym | ||||||
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Title | Backbone Trace of the Capsid Protein Dimer of a Fungal Partitivirus from Electron Cryomicroscopy and Homology Modeling | ||||||
Components | Capsid protein | ||||||
Keywords | VIRUS / dsRNA virus / icosahedral virus / partitivirus / Penicillium stoloniferum virus S / PsV-S | ||||||
Function / homology | Capsid protein Function and homology information | ||||||
Biological species | Penicillium stoloniferum virus S | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||
Authors | Tang, J. / Pan, J. / Havens, W.F. / Ochoa, W.F. / Li, H. / Sinkovits, R.S. / Guu, T.S.Y. / Ghabrial, S.A. / Nibert, M.L. / Tao, J.Y. / Baker, T.S. | ||||||
Citation | Journal: Biophys J / Year: 2010 Title: Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling. Authors: Jinghua Tang / Junhua Pan / Wendy M Havens / Wendy F Ochoa / Tom S Y Guu / Said A Ghabrial / Max L Nibert / Yizhi Jane Tao / Timothy S Baker / Abstract: Most dsRNA viruses have a genome-enclosing capsid that comprises 120 copies of a single coat protein (CP). These 120 CP subunits are arranged as asymmetrical dimers that surround the icosahedral ...Most dsRNA viruses have a genome-enclosing capsid that comprises 120 copies of a single coat protein (CP). These 120 CP subunits are arranged as asymmetrical dimers that surround the icosahedral fivefold axes, forming pentamers of dimers that are thought to be assembly intermediates. This scheme is violated, however, in recent structures of two dsRNA viruses, a fungal virus from family Partitiviridae and a rabbit virus from family Picobirnaviridae, both of which have 120 CP subunits organized as dimers of quasisymmetrical dimers. In this study, we report the CP backbone trace of a second fungal partitivirus, determined in this case by electron cryomicroscopy and homology modeling. This virus also exhibits quasisymmetrical CP dimers that are connected by prominent surface arches and stabilized by domain swapping between the two CP subunits. The CP fold is dominated by alpha-helices, although beta-strands mediate several important contacts. A dimer-of-dimers assembly intermediate is again implicated. The disordered N-terminal tail of each CP subunit protrudes into the particle interior and likely interacts with the genome during packaging and/or transcription. These results broaden our understanding of conserved and variable aspects of partitivirus structure and reflect the growing use of electron cryomicroscopy for atomic modeling of protein folds. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 3iym.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iym.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 3iym.json.gz | Tree view | PDBx/mmJSON format | |
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-Validation report
Summary document | 3iym_validation.pdf.gz | 349.8 KB | Display | wwPDB validaton report |
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Full document | 3iym_full_validation.pdf.gz | 371.2 KB | Display | |
Data in XML | 3iym_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 3iym_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/3iym ftp://data.pdbj.org/pub/pdb/validation_reports/iy/3iym | HTTPS FTP |
-Related structure data
Related structure data | 5161MC 5163MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 46830.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: virus / Source: (natural) Penicillium stoloniferum virus S / Strain: Penicillium stoloniferum virus S / References: UniProt: Q6YDQ6 |
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-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: PsV-S / Type: VIRUS / Details: authentic virus particles |
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Details of virus | Empty: NO / Enveloped: NO / Host category: FUNGI / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Penicillium stoloniferum |
Buffer solution | Name: 50mM Tris pH7.6, 150mM NaCl, 5mM EDTA, 1mM DTT / pH: 7.6 / Details: 50mM Tris pH7.6, 150mM NaCl, 5mM EDTA, 1mM DTT |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 89 K / Humidity: 80 % / Method: blot for 7.5 seconds before plunging |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 20 / Date: Oct 2, 2006 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2.2 nm / Nominal defocus min: 1.4 nm / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Eucentric / Temperature: 77 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software | Name: Auto3DEM / Category: 3D reconstruction | ||||||||||||
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Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 4.7 Å / Num. of particles: 14252 / Nominal pixel size: 1.27 Å / Actual pixel size: 1.27 Å / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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