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- EMDB-5184: The structure of JC polyomavirus treated with 250 mM L-arginine (... -

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Database: EMDB / ID: 5184
TitleThe structure of JC polyomavirus treated with 250 mM L-arginine (pH 10.7)
KeywordsJC / JCV / polyomavirus / arginine
SampleJC polyomavirus in buffer A with 250 mM L-arginine (pH 10.7)
SourceJC polyomavirus / virus / JCV
Map dataCryo-EM based reconstruction of JC polyomavirus treated with 250 mM L-arginine
Methodsingle particle (icosahedral) reconstruction, at 17.6 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
CitationVirology, 2011, 411, 142-152

Virology, 2011, 411, 142-152 Yorodumi Papers
The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4.
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

DateDeposition: Apr 12, 2010 / Header (metadata) release: Dec 8, 2010 / Map release: Jan 19, 2011 / Last update: Sep 23, 2011

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 26
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 26
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_5184.map.gz (map file in CCP4 format, 193091 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
367 pix
1.59 Å/pix.
= 597.84 Å
367 pix
1.59 Å/pix.
= 597.84 Å
367 pix
1.59 Å/pix.
= 597.84 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.59 Å
Contour Level:26 (by author), 26 (movie #1):
Minimum - Maximum-23.6142 - 78.3666
Average (Standard dev.)8.0241 (18.0072)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 597.84 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.591.591.59
M x/y/z376376376
origin x/y/z0.0000.0000.000
length x/y/z597.840597.840597.840
start NX/NY/NZ-34-26-72
MAP C/R/S123
start NC/NR/NS-183-183-183
D min/max/mean-23.61478.3678.024

Supplemental data

Sample components

Entire JC polyomavirus in buffer A with 250 mM L-arginine (pH 10.7)

EntireName: JC polyomavirus in buffer A with 250 mM L-arginine (pH 10.7)
Number of components: 1 / Oligomeric State: virions

Component #1: virus, JC polyomavirus

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

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1.5 mg/ml
Buffer solution: 10 mM Tris, 50 mM NaCl, 0.01 mM CaCl2, 250 mM L-arginine
pH: 10.7
Support film200 mesh copper grid (holey carbon)
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 89 K / Humidity: 100 % / Method: 3 second blot before plunging
Details: Vitrification instrument: Vitrobot. vitrification carried out in nitrogen atmosphere

Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30 / Date: Apr 23, 2007
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 - 4900 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

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.

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: common lines / Software: PFT2 and EM3DR2 / CTF correction: each micrograph / Resolution: 17.6 Å / Resolution method: FSC 0.333

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