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Yorodumi- EMDB-5180: The structure of avian polyomavirus treated with 250 mM L-arginine -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5180 | |||||||||
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Title | The structure of avian polyomavirus treated with 250 mM L-arginine | |||||||||
Map data | Cryo-EM based reconstruction of avian polyomavirus at 11.4-Angstrom resolution. | |||||||||
Sample |
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Keywords | avian / polyomavirus / VP4 | |||||||||
Function / homology | Function and homology information T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | avian polyomavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.4 Å | |||||||||
Authors | Shen PS / Enderlein D / Nelson C / Carter WS / Kawano M / Xing L / Swenson RD / Olson NH / Baker TS / Cheng RH ...Shen PS / Enderlein D / Nelson C / Carter WS / Kawano M / Xing L / Swenson RD / Olson NH / Baker TS / Cheng RH / Atwood WJ / Johne R / Belnap DM | |||||||||
Citation | Journal: Virology / Year: 2011 Title: The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4. Authors: Peter S Shen / Dirk Enderlein / Christian D S Nelson / Weston S Carter / Masaaki Kawano / Li Xing / Robert D Swenson / Norman H Olson / Timothy S Baker / R Holland Cheng / Walter J Atwood / ...Authors: Peter S Shen / Dirk Enderlein / Christian D S Nelson / Weston S Carter / Masaaki Kawano / Li Xing / Robert D Swenson / Norman H Olson / Timothy S Baker / R Holland Cheng / Walter J Atwood / Reimar Johne / David M Belnap / Abstract: Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and ...Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and compared it to that of mammalian polyomaviruses, particularly JC polyomavirus and simian virus 40. The structure of the pentameric major capsid protein (VP1) is mostly conserved; however, APV VP1 has a unique, truncated C-terminus that eliminates an intercapsomere-connecting β-hairpin observed in other polyomaviruses. We postulate that the terminal β-hairpin locks other polyomavirus capsids in a stable conformation and that absence of the hairpin leads to the observed capsid size variation in APV. Plug-like density features were observed at the base of the VP1 pentamers, consistent with the known location of minor capsid proteins VP2 and VP3. However, the plug density is more prominent in APV and may include VP4, a minor capsid protein unique to bird polyomaviruses. | |||||||||
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_5180.map.gz | 91.9 MB | EMDB map data format | |
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Header (meta data) | emd-5180-v30.xml emd-5180.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_5180_1.jpg | 46.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5180 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5180 | HTTPS FTP |
-Validation report
Summary document | emd_5180_validation.pdf.gz | 382.7 KB | Display | EMDB validaton report |
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Full document | emd_5180_full_validation.pdf.gz | 382.3 KB | Display | |
Data in XML | emd_5180_validation.xml.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5180 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5180 | HTTPS FTP |
-Related structure data
Related structure data | 3iysMC 5181C 5182C 5183C 5184C 5187C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5180.map.gz / Format: CCP4 / Size: 184.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM based reconstruction of avian polyomavirus at 11.4-Angstrom resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.57 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 : avian polyomavirus with 250 mM L-arginine
Entire | Name: avian polyomavirus with 250 mM L-arginine |
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Components |
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-Supramolecule #1000: avian polyomavirus with 250 mM L-arginine
Supramolecule | Name: avian polyomavirus with 250 mM L-arginine / type: sample / ID: 1000 / Oligomeric state: virions / Number unique components: 1 |
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-Supramolecule #1: avian polyomavirus
Supramolecule | Name: avian polyomavirus / type: virus / ID: 1 / Name.synonym: avian polyomavirus Details: Cryo-EM of avian polyomavirus over holey carbon grids Sci species name: avian polyomavirus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: avian polyomavirus |
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Host (natural) | synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Name: VP1 / Diameter: 5000 Å / T number (triangulation number): 7 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 10.7 Details: 200 mM NaCl, 20 mM Tris-HCl, 1 mM CaCl2 buffer, 250 mM L-arginine, pH 10.7 |
Grid | Details: 200 mesh copper grid (holey carbon) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: OTHER Details: Vitrification instrument: Vitrobot. vitrification carried out in nitrogen atmosphere Method: 1 second blot before plunging |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Min: 88 K / Max: 95 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: astigmatism was corrected at 59,000 times magnification |
Date | Apr 23, 2007 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 1.57 µm / Number real images: 88 / Details: Micrographs digitized in positive contrast mode. / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 39000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.9 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.4 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: PFT2 and EM3DR2 |