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- PDB-3iys: Homology model of avian polyomavirus asymmetric unit -

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Entry
Database: PDB / ID: 3iys
TitleHomology model of avian polyomavirus asymmetric unit
ComponentsMajor capsid protein VP1
KeywordsVIRUS / avian / polyomavirus / APV / icosahedral virus
Function / homologyDouble-stranded DNA virus, group I, capsid / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / Major capsid protein VP1
Function and homology information
Specimen sourceBudgerigar fledgling disease polyomavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 11.3 Å resolution
AuthorsShen, P.S. / Enderlein, D. / Nelson, C.D.S. / Carter, W.S. / Kawano, M. / Xing, L. / Swenson, R.D. / Olson, N.H. / Baker, T.S. / Cheng, R.H. / Atwood, W.J. / Johne, R. / Belnap, D.M.
CitationJournal: Virology / Year: 2011
Title: The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4.
Authors: Peter S Shen / Dirk Enderlein / Christian D S Nelson / Weston S Carter / Masaaki Kawano / Li Xing / Robert D Swenson / Norman H Olson / Timothy S Baker / R Holland Cheng / Walter J Atwood / Reimar Johne / David M Belnap
Abstract: Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and ...Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and compared it to that of mammalian polyomaviruses, particularly JC polyomavirus and simian virus 40. The structure of the pentameric major capsid protein (VP1) is mostly conserved; however, APV VP1 has a unique, truncated C-terminus that eliminates an intercapsomere-connecting β-hairpin observed in other polyomaviruses. We postulate that the terminal β-hairpin locks other polyomavirus capsids in a stable conformation and that absence of the hairpin leads to the observed capsid size variation in APV. Plug-like density features were observed at the base of the VP1 pentamers, consistent with the known location of minor capsid proteins VP2 and VP3. However, the plug density is more prominent in APV and may include VP4, a minor capsid protein unique to bird polyomaviruses.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 19, 2010 / Release: Jan 26, 2011
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 26, 2011Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jul 18, 2018Structure modelData collectionem_image_scans / em_software_em_software.image_processing_id

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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-5180
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-5180
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
F: Major capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)224,6976
Polyers224,6976
Non-polymers00
Water0
1
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
F: Major capsid protein VP1
x 60


Theoretical massNumber of molelcules
Total (without water)13,481,796360
Polyers13,481,796360
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
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
F: Major capsid protein VP1
x 5


  • icosahedral pentamer
  • 1.12 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,123,48330
Polyers1,123,48330
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
F: Major capsid protein VP1
x 6


  • icosahedral 23 hexamer
  • 1.35 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,348,18036
Polyers1,348,18036
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 / Coordinate model: Cα atoms only


Mass: 37449.434 Da / Num. of mol.: 6 / Source: (natural) Budgerigar fledgling disease polyomavirus / References: UniProt: P13891

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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: avian polyomavirus / Type: VIRUS / Details: Cryo-EM single particle reconstruction
Details of virusVirus host category: VERTEBRATES / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Aves
Buffer solutionName: GP buffer with 250 mM L-arginine / Details: GP buffer with 250 mM L-arginine / pH: 10.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: avian polyomavirus in holey carbon grid
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: APV / Method: 3 second blot

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30 / Date: Apr 23, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 / Calibrated magnification: 39000 / Nominal defocus max: 4900 nm / Nominal defocus min: 500 nm
Astigmatism: astigmatism was corrected at 59,000 times magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder
Temperature: 90 kelvins / Temperature (max): 95 kelvins / Temperature (min): 88 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2PFT3DR3D reconstruction
CTF correctionDetails: full CTF correction (FSC cutoff 0.3)
SymmetryPoint symmetry: I
3D reconstructionMethod: Fourier Bessel / Resolution: 11.3 Å / Number of particles: 5338 / Nominal pixel size: 1.63 / Actual pixel size: 1.57
Magnification calibration: against simian virus 40 atomic coordinates
Symmetry type: POINT
Atomic model buildingDetails: METHOD--rigid body REFINEMENT PROTOCOL--rigid body / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: cross-correlation coefficient
Atomic model buildingPDB-ID: 1SIE
Number of atoms included #LASTProtein: 2004 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2004

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