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- EMDB-3944: BK polyomavirus + 20 mM GT1b oligosaccharide -

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Basic information

Entry
Database: EMDB / ID: 3944
TitleBK polyomavirus + 20 mM GT1b oligosaccharide
Map dataBK polyomavirus in complex with GT1b oligosaccharide.BK virus
SampleBK polyomavirusBK virus:
virus / Capsid protein VP1 / Minor capsid protein VP2 / (ligand) x 2
Function / homologyPolyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Polyomavirus coat protein / Polyomavirus coat protein VP2 / Capsid protein VP1,Polyomavirus / caveolin-mediated endocytosis of virus by host cell / permeabilization of host organelle membrane involved in viral entry into host cell / viral entry via permeabilization of inner membrane / T=7 icosahedral viral capsid ...Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Polyomavirus coat protein / Polyomavirus coat protein VP2 / Capsid protein VP1,Polyomavirus / caveolin-mediated endocytosis of virus by host cell / permeabilization of host organelle membrane involved in viral entry into host cell / viral entry via permeabilization of inner membrane / T=7 icosahedral viral capsid / host cell endoplasmic reticulum membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / viral capsid / viral penetration into host nucleus / ion channel activity / protein complex oligomerization / host cell nucleus / virion attachment to host cell / structural molecule activity / DNA binding / integral component of membrane / Major capsid protein VP1 / Minor capsid protein VP2 / Capsid protein VP1
Function and homology information
SourceHuman polyomavirus 1 / BKPyV (virus)
Methodsingle particle reconstruction / cryo EM / 3.4 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.
Validation ReportPDB-ID: 6esb

SummaryFull reportAbout validation report
DateDeposition: Oct 20, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: May 2, 2018 / Last update: Jun 13, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.046
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.046
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6esb
  • Surface level: 0.046
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6esb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3944.map.gz (map file in CCP4 format, 864001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0651 Å
Density
Contour Level:0.046 (by author), 0.046 (movie #1):
Minimum - Maximum-0.14084125 - 0.25638077
Average (Standard dev.)0.0017956675 (0.013506392)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions600600600
Origin0.00.00.0
Limit599.0599.0599.0
Spacing600600600
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
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.1410.2560.002

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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: 5

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Component #1: virus, Human polyomavirus 1

VirusName: Human polyomavirus 1Polyomaviridae / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Human polyomavirus 1
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: Icosahedron / Diameter: 500.0 Å / T number(triangulation number): 7

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Component #2: protein, Capsid protein VP1

ProteinName: Capsid protein VP1 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 40.053449 kDa
SourceSpecies: BKPyV (virus)

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Component #3: protein, Minor capsid protein VP2

ProteinName: Minor capsid protein VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.25273 kDa
SourceSpecies: BKPyV (virus)

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Component #4: ligand, O-SIALIC ACID

LigandName: O-SIALIC ACID / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.30927 kDa

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Component #5: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

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

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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: 59 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 40334
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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