|Entry||Database: EMDB / ID: 5187|
|Title||Cryo-EM of SV40 Virion|
|Map data||cryo-EM based reconstruction of SV40 virions|
|Sample||simian virus 40SV40:|
|Keywords||SV40 / simian virus 40 / polyomavirus / polyomaviruses|
|Source||Simian virus 40 (SV40)|
|Method||single particle reconstruction / cryo EM / 23 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|
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.
|Date||Deposition: Apr 15, 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_5187.map.gz (map file in CCP4 format, 149504 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.75 Å|
CCP4 map header:
-Entire simian virus 40
|Entire||Name: simian virus 40 / Number of components: 1 / Oligomeric State: virions|
-Component #1: virus, Simian virus 40
|Virus||Name: Simian virus 40SV40 / a.k.a: SV40 / Class: VIRION / Details: Cryo-EM of simian virus 40 over holey carbon grids / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Simian virus 40 (SV40)|
|Source (natural)||Host category: VERTEBRATES|
|Shell #1||Name of element: VP1 / Diameter: 500 Å / T number(triangulation number): 7|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Support film||400 mesh copper grid (holey carbon)|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: blotted for a few seconds before plunging|
Details: Vitrification instrument: homemade. vitrification carried out in normal, room atmosphere
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS EM420|
|Electron gun||Electron source: TUNGSTEN HAIRPIN / Accelerating voltage: 80 kV / Electron dose: 11.5 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 36000 X (nominal), 36300 X (calibrated) / 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
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 10 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 1.75 microns / Bit depth: 16 / Details: Micrographs digitized in positive contrast mode.|
|Processing||Method: single particle reconstruction / Number of projections: 1155 / Details: Particles were selected using X3DPREPROCESS. / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: Fourier Bessel / Software: PFT3DR / CTF correction: each micrograph / Resolution: 23 Å / Resolution method: FSC 0.333|
-Atomic model buiding
|Modeling #1||Software: UCSF Chimera / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL / Details: Protocol: Rigid Body|
Input PDB model: 1SVA
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