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- EMDB-4212: BK polyomavirus + 5 mM dithiothreitol -

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Basic information

Entry
Database: EMDB / ID: EMD-4212
TitleBK polyomavirus + 5 mM dithiothreitol
Map dataBK polyomavirus treated with 5 mM dithiothreitol
Sample
  • Virus: BK polyomavirus
Biological speciesBK polyomavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsHurdiss DL / Ranson NA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust102572/B/13/Z United Kingdom
CitationJournal: Structure / Year: 2018
Title: The Structure of an Infectious Human Polyomavirus and Its Interactions with Cellular Receptors.
Authors: Daniel L Hurdiss / Martin Frank / Joseph S Snowden / Andrew Macdonald / Neil A Ranson /
Abstract: BK polyomavirus (BKV) causes polyomavirus-associated nephropathy and hemorrhagic cystitis in immunosuppressed patients. These are diseases for which we currently have limited treatment options, but ...BK polyomavirus (BKV) causes polyomavirus-associated nephropathy and hemorrhagic cystitis in immunosuppressed patients. These are diseases for which we currently have limited treatment options, but potential therapies could include pre-transplant vaccination with a multivalent BKV vaccine or therapeutics which inhibit capsid assembly or block attachment and entry into target cells. A useful tool in such efforts would be a high-resolution structure of the infectious BKV virion and how this interacts with its full repertoire of cellular receptors. We present the 3.4-Å cryoelectron microscopy structure of native, infectious BKV in complex with the receptor fragment of GT1b ganglioside. We also present structural evidence that BKV can utilize glycosaminoglycans as attachment receptors. This work highlights features that underpin capsid stability and provides a platform for rational design and development of urgently needed pharmacological interventions for BKV-associated diseases.
History
DepositionDec 15, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseMay 2, 2018-
UpdateApr 1, 2020-
Current statusApr 1, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0194
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0194
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4212.png

Downloads & links

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Map

FileDownload / File: emd_4212.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBK polyomavirus treated with 5 mM dithiothreitol
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 600 pix.
= 639.06 Å		1.07 Å/pix.
x 600 pix.
= 639.06 Å		1.07 Å/pix.
x 600 pix.
= 639.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0194 / Movie #1: 0.0194
Minimum - Maximum-0.012182622 - 0.05275681
Average (Standard dev.)0.0031285053 (±0.007836287)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 639.06 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06511.06511.0651
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z639.060639.060639.060
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0120.0530.003

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Supplemental data

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Additional map: BK polyomavirus treated with 5 mM dithiothreitol (unsharpened).

Fileemd_4212_additional.map
AnnotationBK polyomavirus treated with 5 mM dithiothreitol (unsharpened).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BK polyomavirus

EntireName: BK polyomavirus
Components
  • Virus: BK polyomavirus

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Supramolecule #1: BK polyomavirus

SupramoleculeName: BK polyomavirus / type: virus / ID: 1 / Parent: 0 / Details: Vero cells / NCBI-ID: 10629 / Sci species name: BK polyomavirus / Sci species strain: Dunlop / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Icosahedron / Diameter: 500.0 Å / T number (triangulation number): 7

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE
DetailsBK polyomavirus treated with 5 mM dithiothreitol

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Sphere generated in SPIDER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8733
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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