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

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Basic information

Entry
Database: EMDB / ID: EMD-3944
TitleBK polyomavirus + 20 mM GT1b oligosaccharide
Map dataBK polyomavirus in complex with GT1b oligosaccharide.
SampleBK polyomavirus != Human polyomavirus 1

BK polyomavirus

  • Virus: Human polyomavirus 1
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Minor capsid protein VP2
  • Ligand: CALCIUM ION
KeywordsPolyomavirus / Receptor / Complex / Glycan / VIRUS
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / symbiont entry into host cell via permeabilization of host membrane / T=7 icosahedral viral capsid / viral penetration into host nucleus / viral capsid / host cell / channel activity / monoatomic ion transmembrane transport / host cell endoplasmic reticulum membrane / host cell nucleus ...caveolin-mediated endocytosis of virus by host cell / symbiont entry into host cell via permeabilization of host membrane / T=7 icosahedral viral capsid / viral penetration into host nucleus / viral capsid / host cell / channel activity / monoatomic ion transmembrane transport / host cell endoplasmic reticulum membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / DNA binding / membrane
Similarity search - Function
Polyomavirus coat protein VP2 / Polyomavirus coat protein / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein VP1 / Minor capsid protein VP2 / Capsid protein VP1
Similarity search - Component
Biological speciesBK polyomavirus / Human polyomavirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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
DepositionOct 20, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseMay 2, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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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
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6esb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3944.png

Downloads & links

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Map

FileDownload / File: emd_3944.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBK polyomavirus in complex with GT1b oligosaccharide.
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: 0.046 / Movie #1: 0.046
Minimum - Maximum-0.14084125 - 0.25638077
Average (Standard dev.)0.0017956675 (±0.013506392)
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
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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Additional map: BK polyomavirus in complex with GT1b oligosaccharide (unsharpened...

Fileemd_3944_additional.map
AnnotationBK polyomavirus in complex with GT1b oligosaccharide (unsharpened map).
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: Human polyomavirus 1
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Minor capsid protein VP2
  • Ligand: CALCIUM ION

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Supramolecule #1: Human polyomavirus 1

SupramoleculeName: Human polyomavirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 1891762 / Sci species name: Human polyomavirus 1 / 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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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: BK polyomavirus
Molecular weightTheoretical: 40.053449 KDa
SequenceString: APTKRKGECP GAAPKKPKEP VQVPKLLIKG GVEVLEVKTG VDAITEVECF LNPEMGDPDE NLRGFSLKLS AENDFSSDSP ERKMLPCYS TARIPLPNLN EDLTCGNLLM WEAVTVQTEV IGITSMLNLH AGSQKVHEHG GGKPIQGSNF HFFAVGGDPL E MQGVLMNY ...String:
APTKRKGECP GAAPKKPKEP VQVPKLLIKG GVEVLEVKTG VDAITEVECF LNPEMGDPDE NLRGFSLKLS AENDFSSDSP ERKMLPCYS TARIPLPNLN EDLTCGNLLM WEAVTVQTEV IGITSMLNLH AGSQKVHEHG GGKPIQGSNF HFFAVGGDPL E MQGVLMNY RTKYPDGTIT PKNPTAQSQV MNTDHKAYLD KNNAYPVECW VPDPSRNENT RYFGTFTGGE NVPPVLHVTN TA TTVLLDE QGVGPLCKAD SLYVSAADIC GLFTNSSGTQ QWRGLARYFK IRLRKRSVKN PYPISFLLSD LINRRTQRVD GQP MYGMES QVEEVRVFDG TERLPGDPDM IRYIDKQGQL QTKML

UniProtKB: Capsid protein VP1

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Macromolecule #2: Minor capsid protein VP2

MacromoleculeName: Minor capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: BK polyomavirus
Molecular weightTheoretical: 38.25273 KDa
SequenceString: GAALALLGDL VASVSEAAAA TGFSVAEIAA GEAAAAIEVQ IASLATVEGI TSTSEAIAAI GLTPQTYAVI AGAPGAIAGF AALIQTVSG ISSLAQVGYR FFSDWDHKVS TVGLYQQSGM ALELFNPDEY YDILFPGVNT FVNNIQYLDP RHWGPSLFAT I SQALWHVI ...String:
GAALALLGDL VASVSEAAAA TGFSVAEIAA GEAAAAIEVQ IASLATVEGI TSTSEAIAAI GLTPQTYAVI AGAPGAIAGF AALIQTVSG ISSLAQVGYR FFSDWDHKVS TVGLYQQSGM ALELFNPDEY YDILFPGVNT FVNNIQYLDP RHWGPSLFAT I SQALWHVI RDDIPSITSQ ELQRRTERFF RDSLARFLEE TTWTIVNAPI NFYNYIQQYY SDLSPIRPSM VRQVAEREGT RV HFGHTYS IDDADSIEEV TQRMDLRNQQ SVHSGEFIEK TIAPGGANQR TAPQWMLPLL LGLYGTVTPA LEAYEDGPNQ KKR RVSRGS SQKAKGTRAS AKTTNKRRSR SSRS

UniProtKB: Minor capsid protein VP2

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 59.0 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40334
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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