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

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Basic information

Database: EMDB / ID: 4212
TitleBK polyomavirus + 5 mM dithiothreitol
Map dataBK polyomavirus treated with 5 mM dithiothreitol
SampleBK polyomavirusBK virus:
SourceBK polyomavirus
Methodsingle particle reconstruction / cryo EM / 6.5 Å resolution
AuthorsHurdiss DL / Ranson NA
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.
DateDeposition: Dec 15, 2017 / Header (metadata) release: Jan 17, 2018 / Map release: May 2, 2018 / Last update: Jun 13, 2018

Structure visualization

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

Downloads & links


Fileemd_4212.map.gz (map file in CCP4 format, 864001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
1.07 Å/pix.
= 639.06 Å
600 pix
1.07 Å/pix.
= 639.06 Å
600 pix
1.07 Å/pix.
= 639.06 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0651 Å
Contour Level:0.0194 (by author), 0.0194 (movie #1):
Minimum - Maximum-0.012182622 - 0.05275681
Average (Standard dev.)0.0031285053 (0.007836287)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 639.06 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0120.0530.003

Supplemental data

Sample components

Entire BK polyomavirus

EntireName: BK polyomavirus / Details: Vero cells / Number of components: 1

Component #1: virus, BK polyomavirus

VirusName: BK polyomavirusBK virus / Class: VIRION / Details: Vero cells / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: BK polyomavirus / Strain: Dunlop
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: Icosahedron / Diameter: 500.0 Å / T number(triangulation number): 7

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.25 mg/ml / pH: 7.5
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 66 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 8733
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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