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

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Basic information

Entry
Database: EMDB / ID: 3283
TitleCryo-EM structure of BK polyomavirus
Map dataReconstruction of BK polyomavirus (sharpened/masked)
SampleBK polyomavirusBK virus:
virus
KeywordsBKPyV / BK / polyomavirus
Function / homologyDouble-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 / virion attachment to host cell / host cell nucleus / structural molecule activity / Major capsid protein VP1
Function and homology information
SourceBK polyomavirus
Methodsingle particle reconstruction / cryo EM / 7.6 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.
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

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Structure visualization

Movie
  • 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

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

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin-192-192-192
Limit191191191
Spacing384384384
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
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-0.0230.0540.001

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Supplemental data

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Sample components

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Entire BK polyomavirus

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

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Component #1: virus, BK polyomavirus

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
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

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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
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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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

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Image processing

ProcessingMethod: single particle 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 estimation)

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Atomic model buiding

Output model

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