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- EMDB-3283: Cryo-EM structure of BK polyomavirus -

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Basic information

Database: EMDB / ID: 3283
TitleCryo-EM structure of BK polyomavirus
KeywordsBKPyV / BK / polyomavirus
SampleBK polyomavirus
SourceBK polyomavirus / virus
Map dataReconstruction of BK polyomavirus (sharpened/masked)
Methodsingle particle (icosahedral) reconstruction, at 7.6 Å resolution
AuthorsHurdiss DL / Morgan EL / Thompson RF / Prescott EL / Panou MM / Macdonald A / Ranson NA
CitationStructure, 2016, 24, 528-536

Structure, 2016, 24, 528-536 Yorodumi Papers
New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy.
Daniel L Hurdiss / Ethan L Morgan / Rebecca F Thompson / Emma L Prescott / Margarita M Panou / Andrew Macdonald / Neil A Ranson

Validation ReportPDB-ID: 5fua

SummaryFull reportAbout validation report
DateDeposition: Dec 17, 2015 / Header (metadata) release: Jan 13, 2016 / Map release: Apr 27, 2016 / Last update: May 18, 2016

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 0.022
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5fua
  • Surface level: 0.022
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5fua
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links


Fileemd_3283.map.gz (map file in CCP4 format, 221185 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.92 Å/pix.
= 737.28 Å
384 pix
1.92 Å/pix.
= 737.28 Å
384 pix
1.92 Å/pix.
= 737.28 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.92 Å
Contour Level:0.022 (by author), 0.022 (movie #1):
Minimum - Maximum-0.02264674 - 0.05379711
Average (Standard dev.)0.00088005 (0.00504107)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 737.27997 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.921.921.92
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z737.280737.280737.280
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-192-192-192
D min/max/mean-0.0230.0540.001

Supplemental data

Sample components

Entire BK polyomavirus

EntireName: BK polyomavirus / Number of components: 1 / Oligomeric State: Icosohedral

Component #1: virus, BK polyomavirus

VirusName: BK polyomavirus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: BK polyomavirus / virus / Strain: Dunlop
Source (engineered)Cell of expression system: Vero cells
Source (natural)Host Species: Homo sapiens / human / Wikipedia / Host category: VERTEBRATES

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 10mM HEPES pH 7.9, 1mM CaCl2, 1mM MgCl2, 5mM KCl
pH: 7.9
Support filmQuantifoil R2/1 EM grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: 6.5 seconds blot before plunging

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Dec 15, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 19000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 600 - 4800 nm
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 432
Details: 4 e-/A2/s, a 4 frames per second frame rate, and a 10 s exposure

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2237
3D reconstructionSoftware: Relion / CTF correction: CTFFIND3 / Resolution: 7.6 Å / Resolution method: FSC 0.143, gold-standard
FSC plot (resolution assessment)

Atomic model buiding

Output model

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