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- EMDB-5187: Cryo-EM of SV40 Virion -

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Basic information

Entry
Database: EMDB / ID: 5187
TitleCryo-EM of SV40 Virion
Map datacryo-EM based reconstruction of SV40 virions
Samplesimian virus 40SV40:
virus
KeywordsSV40 / simian virus 40 / polyomavirus / polyomaviruses
SourceSimian virus 40 (SV40)
Methodsingle particle reconstruction / cryo EM / 23 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
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.
#1: Journal: J.MOL.BIOL.
Title: Conserved features in papillomavirus and polyomavirus capsids
Authors: Belnap DM / Olson NH / Cladel NM / Newcomb WW / Brown JC / Kreider JW / Christensen ND / Baker TS
DateDeposition: Apr 15, 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: 151
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 151
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5187.map.gz (map file in CCP4 format, 149504 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
337 pix
1.75 Å/pix.
= 593.25 Å
337 pix
1.75 Å/pix.
= 593.25 Å
337 pix
1.75 Å/pix.
= 593.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.75 Å
Density
Contour Level:151 (by author), 151 (movie #1):
Minimum - Maximum-43.6475 - 306.354
Average (Standard dev.)56.9662 (93.6761)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions337337337
Origin-168-168-168
Limit168168168
Spacing337337337
CellA=B=C: 593.25 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.751.751.75
M x/y/z339339339
origin x/y/z0.0000.0000.000
length x/y/z593.250593.250593.250
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-168-168-168
NC/NR/NS337337337
D min/max/mean-43.647306.35456.966

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Supplemental data

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Sample components

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Entire simian virus 40

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

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Component #1: virus, Simian virus 40

VirusName: 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
SpeciesSpecies: Simian virus 40 (SV40)
Source (natural)Host category: VERTEBRATES
Shell #1Name of element: VP1 / Diameter: 500 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 solutionpH: 7.4
Support film400 mesh copper grid (holey carbon)
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: blotted for a few seconds before plunging
Details: Vitrification instrument: homemade. vitrification carried out in normal, room atmosphere

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS EM420
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 80 kV / Electron dose: 11.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 36000 X (nominal), 36300 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 4900 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 10 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 1.75 microns / Bit depth: 16 / Details: Micrographs digitized in positive contrast mode.

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1155 / Details: Particles were selected using X3DPREPROCESS. / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Fourier Bessel / Software: PFT3DR / CTF correction: each micrograph / Resolution: 23 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
Input PDB model: 1SVA

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