|Entry||Database: EMDB / ID: EMD-5183|
|Title||The structure of JC polyomavirus (pH 7.4)|
|Sample||JC polyomavirus in buffer A (pH 7.4):|
|Keywords||JC / JCV / polyomavirus|
|Biological species||JC polyomavirus (JCV)|
|Method||single particle reconstruction / cryo EM / Resolution: 19 Å|
|Authors||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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_5183.map.gz / Format: CCP4 / Size: 184.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.62 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire JC polyomavirus in buffer A (pH 7.4)
|Entire||Name: JC polyomavirus in buffer A (pH 7.4) / Number of components: 1 / Oligomeric State: virions|
-Component #1: virus, JC polyomavirus
|Virus||Name: JC polyomavirus / a.k.a: JCV / Class: VIRION / Details: Cryo-EM of JC polyomavirus over holey carbon grids / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: JC polyomavirus (JCV)|
|Source (natural)||Host Species: Homo sapiens (human) / Host category: VERTEBRATES|
|Shell #1||Name of element: VP1 / Diameter: 5000 Å / T number (triangulation number): 7|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 1.5 mg/mL / Buffer solution: 10 mM Tris, 50 mM NaCl, 0.01 mM CaCl2 / pH: 7.4|
|Support film||200 mesh copper grid (holey carbon)|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 89 K / Humidity: 100 % / Method: 3 second blot before plunging|
Details: Vitrification instrument: Vitrobot. vitrification carried out in nitrogen atmosphere
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30 / Date: Apr 23, 2007|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 39000 X (nominal), 39000 X (calibrated)|
Astigmatism: astigmatism was corrected at 59,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 4900 nm
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN / Temperature: 90 (88 - 95 K)
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 50 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 µm / Bit depth: 16 / Details: Micrographs digitized in positive contrast mode.|
|Processing||Method: single particle reconstruction / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: common lines / Software: PFT2, EM3DR2 / CTF correction: each micrograph / Resolution: 19 Å / Resolution method: FSC 0.333|
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