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- PDB-5fua: Cryo-EM of BK polyomavirus -

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Entry
Database: PDB / ID: 5fua
TitleCryo-EM of BK polyomavirus
ComponentsMAJOR CAPSID PROTEIN VP1
KeywordsVIRUS / BKPYV / 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
Specimen sourceBK POLYOMAVIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.6 Å resolution
AuthorsHurdiss, D.L. / Morgan, E.L. / Thompson, R.F. / Prescott, E.L. / Panou, M.M. / Macdonald, A. / Ranson, N.A.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jan 22, 2016 / Release: Apr 20, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 20, 2016Structure modelrepositoryInitial release
2.0Oct 3, 2018Structure modelAtomic model / Data collectionatom_site / em_software_atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-3283
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-3283
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: MAJOR CAPSID PROTEIN VP1
2: MAJOR CAPSID PROTEIN VP1
3: MAJOR CAPSID PROTEIN VP1
4: MAJOR CAPSID PROTEIN VP1
5: MAJOR CAPSID PROTEIN VP1
6: MAJOR CAPSID PROTEIN VP1


Theoretical massNumber of molelcules
Total (without water)240,9286
Polyers240,9286
Non-polymers00
Water0
1
1: MAJOR CAPSID PROTEIN VP1
2: MAJOR CAPSID PROTEIN VP1
3: MAJOR CAPSID PROTEIN VP1
4: MAJOR CAPSID PROTEIN VP1
5: MAJOR CAPSID PROTEIN VP1
6: MAJOR CAPSID PROTEIN VP1
x 60


Theoretical massNumber of molelcules
Total (without water)14,455,662360
Polyers14,455,662360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: MAJOR CAPSID PROTEIN VP1
2: MAJOR CAPSID PROTEIN VP1
3: MAJOR CAPSID PROTEIN VP1
4: MAJOR CAPSID PROTEIN VP1
5: MAJOR CAPSID PROTEIN VP1
6: MAJOR CAPSID PROTEIN VP1
x 5


  • icosahedral pentamer
  • 1.2 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,204,63930
Polyers1,204,63930
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: MAJOR CAPSID PROTEIN VP1
2: MAJOR CAPSID PROTEIN VP1
3: MAJOR CAPSID PROTEIN VP1
4: MAJOR CAPSID PROTEIN VP1
5: MAJOR CAPSID PROTEIN VP1
6: MAJOR CAPSID PROTEIN VP1
x 6


  • icosahedral 23 hexamer
  • 1.45 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,445,56636
Polyers1,445,56636
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide
MAJOR CAPSID PROTEIN VP1 / / MAJOR STRUCTURAL PROTEIN VP1 / BK POLYOMAVIRUS VP1 ASYMMETRIC UNIT


Mass: 40154.617 Da / Num. of mol.: 6 / Source: (natural) BK POLYOMAVIRUS / Strain: DUNLOP / References: UniProt: P03088

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BK POLYOMAVIRUSBK virus / Type: VIRUS
Buffer solutionName: 10MM HEPES PH 7.9, 1MM CACL2, 1MM MGCL2, 5MM KCL / Details: 10MM HEPES PH 7.9, 1MM CACL2, 1MM MGCL2, 5MM KCL / pH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: 6.5 SECONDS BLOT BEFORE PLUNGING IN LIQUID ETHAN

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Dec 15, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 19000 / Nominal defocus max: 4800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNumber digital images: 432

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: CTFFIND3
SymmetryPoint symmetry: I
3D reconstructionResolution: 7.6 Å / Number of particles: 2237
Details: A HOMOLOGY MODEL OF THE BKPYV VP1 ASYMMETRIC UNIT BASED ON THE CRYSTAL STRUCTURE OF SV40 (PDB 1SVA) WAS BUILT USING THE SWISS-MODEL SERVER. THIS WAS THEN FITTED (AS A RIGID BODY) INTO A CORRESPONDING SEGMENT OF THE BKPYV CRYO-EM DENSITY MAP GENERATED USING UCSF CHIMERA. FLEXIBLE FITTING OF THE HOMOLOGY MODEL WAS THEN CARRIED OUT USING MDFF (TRABUCO ET AL. 10 2008). SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3283. (DEPOSITION ID: 14117).
Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--HOMOLOGY MODEL / Ref protocol: OTHER
Least-squares processHighest resolution: 7.6 Å
Refine hist #LASTHighest resolution: 7.6 Å
Number of atoms included #LASTProtein: 16042 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 16042

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