|Entry||Database: EMDB / ID: 5180|
|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||avian polyomavirus with 250 mM L-arginine:|
|Keywords||avian / polyomavirus / VP4|
|Function / homology||Double-stranded DNA virus, group I, capsid / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / Major capsid protein VP1|
Function and homology information
|Source||avian polyomavirus (avian polyomavirus)|
|Method||single particle reconstruction / cryo EM / 11.4 Å resolution|
|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 / 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.
|Validation Report||PDB-ID: 3iys|
SummaryFull reportAbout validation report
|Date||Deposition: Apr 9, 2010 / Header (metadata) release: Dec 8, 2010 / Map release: Jan 19, 2011 / Last update: Sep 23, 2011|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5180.map.gz (map file in CCP4 format, 193091 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.57 Å|
CCP4 map header:
-Entire avian polyomavirus with 250 mM L-arginine
|Entire||Name: avian polyomavirus with 250 mM L-arginine / Number of components: 1 / Oligomeric State: virions|
-Component #1: virus, avian polyomavirus
|Virus||Name: avian polyomavirus / a.k.a: avian polyomavirus / Class: VIRION|
Details: Cryo-EM of avian polyomavirus over holey carbon grids
Empty: No / Enveloped: No / Isolate: STRAIN
|Species||Species: avian polyomavirus (avian polyomavirus)|
|Source (natural)||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: 200 mM NaCl, 20 mM Tris-HCl, 1 mM CaCl2 buffer, 250 mM L-arginine, pH 10.7
|Support film||200 mesh copper grid (holey carbon)|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 89 K / Humidity: 100 % / Method: 1 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 K ( 88 - 95 K)
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 88 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 1.57 microns / 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: 11.4 Å / Resolution method: FSC 0.333|
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