[English] 日本語
Yorodumi
- EMDB-3944: BK polyomavirus + 20 mM GT1b oligosaccharide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3944
TitleBK polyomavirus + 20 mM GT1b oligosaccharide
Map dataBK polyomavirus in complex with GT1b oligosaccharide.BK virus
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 IONCalcium
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / : / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / T=7 icosahedral viral capsid / : / viral penetration into host nucleus / viral capsid / protein complex oligomerization / monoatomic ion channel activity ...caveolin-mediated endocytosis of virus by host cell / : / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / T=7 icosahedral viral capsid / : / viral penetration into host nucleus / viral capsid / protein complex oligomerization / monoatomic ion channel activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell nucleus / structural molecule activity / virion attachment to host cell / DNA binding
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 speciesBKPyV (virus) / 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-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

-
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
  • Download
  • 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 modelsPDB-6esb
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3944.png

Downloads & links

-
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.
Voxel sizeX=Y=Z: 1.0651 Å
Density
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

-
Supplemental data

-
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)

-
Sample components

-
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 IONCalcium

-
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

-
Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: BKPyV (virus)
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

-
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: BKPyV (virus)
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

-
Macromolecule #4: CALCIUM ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 59.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: Sphere generated in SPIDER
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
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
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more