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

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Basic information

Entry
Database: EMDB / ID: EMD-5187
TitleCryo-EM of SV40 Virion
Map datacryo-EM based reconstruction of SV40 virions
Sample
  • Sample: simian virus 40
  • Virus: Simian virus 40
KeywordsSV40 / simian virus 40 / polyomavirus / polyomaviruses
Biological speciesSimian virus 40
Methodsingle particle reconstruction / cryo EM / Resolution: 23.0 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
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 / ...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
History
DepositionApr 15, 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: 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

emd_5187_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5187.map.gz / Format: CCP4 / Size: 142.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM based reconstruction of SV40 virions
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 151.0 / Movie #1: 151
Minimum - Maximum-43.647500000000001 - 306.353999999999985
Average (Standard dev.)56.966200000000001 (±93.676100000000005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-168-168-168
Dimensions337337337
Spacing337337337
CellA=B=C: 593.25 Å
α=β=γ: 90 °

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
Components
  • Sample: simian virus 40
  • Virus: Simian virus 40

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Supramolecule #1000: simian virus 40

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

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Supramolecule #1: Simian virus 40

SupramoleculeName: Simian virus 40 / type: virus / ID: 1 / Name.synonym: SV40 / Details: Cryo-EM of simian virus 40 over holey carbon grids / NCBI-ID: 10633 / Sci species name: Simian virus 40 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: SV40
Host (natural)synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: VP1 / Diameter: 500 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

BufferpH: 7.4
GridDetails: 400 mesh copper grid (holey carbon)
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: homemade. vitrification carried out in normal, room atmosphere
Method: blotted for a few seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS EM420
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 1.75 µm / Number real images: 10 / Average electron dose: 11.5 e/Å2 / Details: Micrographs digitized in positive contrast mode. / Bits/pixel: 16
Electron beamAcceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 36300 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.9 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 36000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsParticles were selected using X3DPREPROCESS.
CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: PFT3DR / Number images used: 1155

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Atomic model buiding 1

Initial modelPDB ID:

1sva

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor

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