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- EMDB-3284: Cryo-EM structure of BK polyomavirus VP1 virus-like particle -

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Basic information

Database: EMDB / ID: 3284
TitleCryo-EM structure of BK polyomavirus VP1 virus-like particle
Map dataReconstruction of BK VP1 VLP (sharpened/masked)
SampleBK polyomavirus VP1 VLP:
KeywordsBKPyV / BK / polyomavirus / virus-like particle / VLP
SourceBK polyomavirus VP1 VLP
Methodsingle particle reconstruction / cryo EM / 9.12 Å resolution
AuthorsHurdiss DL / Morgan EL / Thompson RF / Prescott EL / Panou MM / Macdonald A / Ranson NA
CitationJournal: Structure / Year: 2016
Title: New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy.
Authors: Daniel L Hurdiss / Ethan L Morgan / Rebecca F Thompson / Emma L Prescott / Margarita M Panou / Andrew Macdonald / Neil A Ranson
Abstract: BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious ...BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious virions and VP1-only virus-like particles in cell culture, and determined their three-dimensional structures using cryo-electron microscopy (EM) and single-particle image processing. The resulting 7.6-Å resolution structure of BK and 9.1-Å resolution of the virus-like particles are the highest-resolution cryo-EM structures of any polyomavirus. These structures confirm that the architecture of the major structural protein components of these human polyomaviruses are similar to previous structures from other hosts, but give new insight into the location and role of the enigmatic minor structural proteins, VP2 and VP3. We also observe two shells of electron density, which we attribute to a structurally ordered part of the viral genome, and discrete contacts between this density and both VP1 and the minor capsid proteins.
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: 0.009
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_3284.map.gz (map file in CCP4 format, 488283 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
500 pix
1.35 Å/pix.
= 675. Å
500 pix
1.35 Å/pix.
= 675. Å
500 pix
1.35 Å/pix.
= 675. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Contour Level:0.009 (by author), 0.009 (movie #1):
Minimum - Maximum-0.00716442 - 0.01983405
Average (Standard dev.)0.00076196 (0.00246748)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 675.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z675.000675.000675.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-249-249-249
D min/max/mean-0.0070.0200.001

Supplemental data

Sample components

Entire BK polyomavirus VP1 VLP

EntireName: BK polyomavirus VP1 VLP / Number of components: 1 / Oligomeric State: Icosohedral

Component #1: virus, BK polyomavirus VP1 VLP

VirusName: BK polyomavirus VP1 VLP / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: BK polyomavirus VP1 VLP / Strain: BKV-Ia
Source (engineered)Vector: pIaw / Cell of expression system: HEK293TT
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 10mM HEPES pH 7.9, 50mM 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 Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: May 13, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 19000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 526 - 6136 nm
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 170
Details: 4 e-/A2/s, a 4 frames per second frame rate, and a 10 s exposure

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2888
3D reconstructionSoftware: Relion / CTF correction: CTFFIND3 / Resolution: 9.12 Å / Resolution method: FSC 0.143, gold-standard
FSC plot
(resolution estimation)

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