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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: EMD-5182
TitleThe structure of simian virus 40 virus-like particles
Map dataCryo-EM based reconstruction of simian virus 40 virus-like particles
Sample
  • Sample: simian virus 40 virus-like particles
  • Virus: avian polyomavirus
KeywordsSV40 / simian virus 40 / virus-like particles
Biological speciesavian polyomavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 13.8 Å
AuthorsShen PS / Enderlein D / Nelson C / Carter WS / Kawano M / Xing L / Swenson RD / Olson NH / Baker TS / Cheng RH ...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
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 / ...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.
History
DepositionApr 9, 2010-
Header (metadata) releaseDec 8, 2010-
Map releaseJan 19, 2011-
UpdateSep 23, 2011-
Current statusSep 23, 2011Processing site: RCSB / Status: Released

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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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5182_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5182.map.gz / Format: CCP4 / Size: 184.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM based reconstruction of simian virus 40 virus-like particles
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 30.0 / Movie #1: 30
Minimum - Maximum-16.259899999999998 - 54.999299999999998
Average (Standard dev.)4.14738 (±12.9438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-183-183-183
Dimensions367367367
Spacing367367367
CellA=B=C: 598.92 Å
α=β=γ: 90 °

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
Components
  • Sample: simian virus 40 virus-like particles
  • Virus: avian polyomavirus

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Supramolecule #1000: simian virus 40 virus-like particles

SupramoleculeName: simian virus 40 virus-like particles / type: sample / ID: 1000 / Oligomeric state: virions / Number unique components: 1

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Supramolecule #1: avian polyomavirus

SupramoleculeName: avian polyomavirus / type: virus / ID: 1 / Name.synonym: avian polyomavirus / Details: Cryo-EM of simian virus 40 over holey carbon grids / Sci species name: avian polyomavirus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: avian polyomavirus
Host (natural)synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: VP1 / Diameter: 5000 Å / T number (triangulation number): 7

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.6 / Details: 20 mM Tris-Cl (pH 7.9) and 50 mM NaCl
GridDetails: 200 mesh copper grid (holey carbon)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: OTHER
Details: Vitrification instrument: Vitrobot. vitrification carried out in nitrogen atmosphere
Method: 4 second blot before plunging

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 88 K / Max: 95 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: astigmatism was corrected at 59,000 times magnification
DateJan 23, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 50 / Details: Micrographs digitized in positive contrast mode. / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.8 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: PFT2 and EM3DR2

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Atomic model buiding 1

Initial modelPDB ID:

1sva

SoftwareName: UCSF Chimera
DetailsProtocol: rigid body. Coordinates were fitted by rigid-body fitting using UCSF Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 20 / Target criteria: R-factor

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