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- EMDB-5182: The structure of simian virus 40 virus-like particles -

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Basic information

Entry
Database: EMDB / ID: 5182
TitleThe structure of simian virus 40 virus-like particles
Map dataCryo-EM based reconstruction of simian virus 40 virus-like particles
Samplesimian virus 40 virus-like particles:
virus
KeywordsSV40 / simian virus 40 / virus-like particles
Sourceavian polyomavirus (avian polyomavirus)
Methodsingle particle reconstruction / cryo EM / 13.8 Å resolution
AuthorsShen 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
CitationJournal: 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.
DateDeposition: Apr 9, 2010 / Header (metadata) release: Dec 8, 2010 / Map release: Jan 19, 2011 / Last update: Sep 23, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 30
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5182.map.gz (map file in CCP4 format, 193091 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
367 pix
1.61 Å/pix.
= 598.92 Å
367 pix
1.61 Å/pix.
= 598.92 Å
367 pix
1.61 Å/pix.
= 598.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.61 Å
Density
Contour Level:30.0 (by author), 30 (movie #1):
Minimum - Maximum-16.2599 - 54.9993
Average (Standard dev.)4.14738 (12.9438)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions367367367
Origin-183-183-183
Limit183183183
Spacing367367367
CellA=B=C: 598.92 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.611.611.61
M x/y/z372372372
origin x/y/z0.0000.0000.000
length x/y/z598.920598.920598.920
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-183-183-183
NC/NR/NS367367367
D min/max/mean-16.26054.9994.147

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Supplemental data

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Sample components

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Entire simian virus 40 virus-like particles

EntireName: simian virus 40 virus-like particles / Number of components: 1 / Oligomeric State: virions

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Component #1: virus, avian polyomavirus

VirusName: avian polyomavirus / a.k.a: avian polyomavirus / Class: VIRION / Details: Cryo-EM of simian virus 40 over holey carbon grids / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: avian polyomavirus (avian polyomavirus)
Source (natural)Host category: VERTEBRATES
Shell #1Name of element: VP1 / Diameter: 5000 Å / T number(triangulation number): 7

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/ml / Buffer solution: 20 mM Tris-Cl (pH 7.9) and 50 mM NaCl / pH: 7.6
Support film200 mesh copper grid (holey carbon)
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 89 K / Humidity: 100 % / Method: 4 second blot before plunging
Details: Vitrification instrument: Vitrobot. vitrification carried out in nitrogen atmosphere

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30 / Date: Jan 23, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensMagnification: 39000 X (nominal), 39000 X (calibrated)
Astigmatism: astigmatism was corrected at 59,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 3500 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 90 K ( 88 - 95 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 50 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16 / Details: Micrographs digitized in positive contrast mode.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: common lines / Software: PFT2, EM3DR2 / CTF correction: each micrograph / Resolution: 13.8 Å / Resolution method: FSC 0.333

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Atomic model buiding

Modeling #1Software: UCSF Chimera / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL
Details: Protocol: rigid body. Coordinates were fitted by rigid-body fitting using UCSF Chimera
Input PDB model: 1SVA
Overall bvalue: 20

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