|Entry||Database: EMDB / ID: 3283|
|Title||Cryo-EM structure of BK polyomavirus|
|Map data||Reconstruction of BK polyomavirus (sharpened/masked)|
|Sample||BK polyomavirusBK virus:|
|Keywords||BKPyV / BK / polyomavirus|
|Function / homology||Double-stranded DNA virus, group I, capsid / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / Major capsid protein VP1|
Function and homology information
|Method||single particle reconstruction / cryo EM / 7.6 Å resolution|
|Authors||Hurdiss DL / Morgan EL / Thompson RF / Prescott EL / Panou MM / Macdonald A / Ranson NA|
|Citation||Journal: 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.
|Validation Report||PDB-ID: 5fua|
SummaryFull reportAbout validation report
|Date||Deposition: Dec 17, 2015 / Header (metadata) release: Jan 13, 2016 / Map release: Apr 27, 2016 / Last update: May 18, 2016|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3283.map.gz (map file in CCP4 format, 221185 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.92 Å|
CCP4 map header:
-Entire BK polyomavirus
|Entire||Name: BK polyomavirus / Number of components: 1 / Oligomeric State: Icosohedral|
-Component #1: virus, BK polyomavirus
|Virus||Name: BK polyomavirusBK virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: BK polyomavirus / Strain: Dunlop|
|Source (engineered)||Cell of expression system: Vero cells|
|Source (natural)||Host Species: Homo sapiens (human) / Host category: VERTEBRATES|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: 10mM HEPES pH 7.9, 1mM CaCl2, 1mM MgCl2, 5mM KCl|
|Support film||Quantifoil R2/1 EM grids|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: 6.5 seconds blot before plunging|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Dec 15, 2014|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 19000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 600 - 4800 nm|
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 432|
Details: 4 e-/A2/s, a 4 frames per second frame rate, and a 10 s exposure
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