[English] 日本語
- EMDB-3283: Cryo-EM structure of BK polyomavirus -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 3283
TitleCryo-EM structure of BK polyomavirus
Map dataReconstruction of BK polyomavirus (sharpened/masked)
SampleBK polyomavirusBK virus:
KeywordsBKPyV / BK / polyomavirus
Function / homologyDouble-stranded DNA virus, group I, capsid / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / Major capsid protein VP1
Function and homology information
SourceBK polyomavirus
Methodsingle particle reconstruction / cryo EM / 7.6 Å resolution
AuthorsHurdiss DL / Morgan EL / Thompson RF / Prescott EL / Panou MM / Macdonald A / Ranson NA
CitationJournal: Structure / Year: 2016
Title: New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy.
Authors: Daniel L Hurdiss / Ethan L Morgan / Rebecca F Thompson / Emma L Prescott / Margarita M Panou / Andrew Macdonald / Neil A Ranson
Abstract: BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious ...BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious virions and VP1-only virus-like particles in cell culture, and determined their three-dimensional structures using cryo-electron microscopy (EM) and single-particle image processing. The resulting 7.6-Å resolution structure of BK and 9.1-Å resolution of the virus-like particles are the highest-resolution cryo-EM structures of any polyomavirus. These structures confirm that the architecture of the major structural protein components of these human polyomaviruses are similar to previous structures from other hosts, but give new insight into the location and role of the enigmatic minor structural proteins, VP2 and VP3. We also observe two shells of electron density, which we attribute to a structurally ordered part of the viral genome, and discrete contacts between this density and both VP1 and the minor capsid proteins.
Validation ReportPDB-ID: 5fua

SummaryFull reportAbout validation report
DateDeposition: Dec 17, 2015 / Header (metadata) release: Jan 13, 2016 / Map release: Apr 27, 2016 / Last update: May 18, 2016

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5fua
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5fua
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_3283.map.gz (map file in CCP4 format, 221185 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.92 Å/pix.
= 737.28 Å
384 pix
1.92 Å/pix.
= 737.28 Å
384 pix
1.92 Å/pix.
= 737.28 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.92 Å
Contour Level:0.022 (by author), 0.022 (movie #1):
Minimum - Maximum-0.02264674 - 0.05379711
Average (Standard dev.)0.00088005 (0.00504107)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 737.27997 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.921.921.92
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z737.280737.280737.280
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-192-192-192
D min/max/mean-0.0230.0540.001

Supplemental data

Sample components

Entire BK polyomavirus

EntireName: BK polyomavirus / Number of components: 1 / Oligomeric State: Icosohedral

Component #1: virus, BK polyomavirus

VirusName: BK polyomavirusBK virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: BK polyomavirus / Strain: Dunlop
Source (engineered)Cell of expression system: Vero cells
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 10mM HEPES pH 7.9, 1mM CaCl2, 1mM MgCl2, 5mM KCl
pH: 7.9
Support filmQuantifoil R2/1 EM grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: 6.5 seconds blot before plunging

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Dec 15, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 19000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 600 - 4800 nm
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 432
Details: 4 e-/A2/s, a 4 frames per second frame rate, and a 10 s exposure

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2237
3D reconstructionSoftware: Relion / CTF correction: CTFFIND3 / Resolution: 7.6 Å / Resolution method: FSC 0.143, gold-standard
FSC plot
(resolution estimation)

Atomic model buiding

Output model

About Yorodumi


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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more


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.

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