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- EMDB-5183: The structure of JC polyomavirus (pH 7.4) -

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Basic information

Database: EMDB / ID: 5183
TitleThe structure of JC polyomavirus (pH 7.4)
Map dataCryo-EM reconstruction of JC polyomavirus (pH 7.4)
SampleJC polyomavirus in buffer A (pH 7.4):
KeywordsJC / JCV / polyomavirus
SourceJC polyomavirus (JCV)
Methodsingle particle reconstruction / cryo EM / 19 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 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: 43
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 43
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_5183.map.gz (map file in CCP4 format, 193091 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
367 pix
1.62 Å/pix.
= 597.78 Å
367 pix
1.62 Å/pix.
= 597.78 Å
367 pix
1.62 Å/pix.
= 597.78 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Contour Level:43.0 (by author), 43 (movie #1):
Minimum - Maximum-72.7188 - 139.522
Average (Standard dev.)10.425 (32.6366)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 597.78 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.621.621.62
M x/y/z369369369
origin x/y/z0.0000.0000.000
length x/y/z597.780597.780597.780
start NX/NY/NZ-34-26-72
MAP C/R/S123
start NC/NR/NS-183-183-183
D min/max/mean-72.719139.52210.425

Supplemental data

Sample components

Entire JC polyomavirus in buffer A (pH 7.4)

EntireName: JC polyomavirus in buffer A (pH 7.4) / 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 (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

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/ml / Buffer solution: 10 mM Tris, 50 mM NaCl, 0.01 mM CaCl2 / pH: 7.4
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 reconstruction / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: common lines / Software: PFT2, EM3DR2 / CTF correction: each micrograph / Resolution: 19 Å / Resolution method: FSC 0.333

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