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

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Basic information

Entry
Database: PDB / ID: 3iys
TitleHomology model of avian polyomavirus asymmetric unit
ComponentsMajor capsid protein VP1
KeywordsVIRUS / avian / polyomavirus / APV / icosahedral virus
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Double-stranded DNA virus, group I, capsid / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein
Major capsid protein VP1
Biological speciesBudgerigar fledgling disease polyomavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.3 Å
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 / ...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
History
DepositionApr 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _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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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polymers224,6976
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
Polymers13,481,796360
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
Polymers1,123,48330
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
Polymers1,348,18036
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major capsid protein VP1 / / Major structural protein VP1 / Coordinate model: Cα atoms only


Mass: 37449.434 Da / Num. of mol.: 6 / Source method: isolated from a natural source / 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 / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: avian polyomavirus / Type: VIRUS / Details: Cryo-EM single particle reconstruction
Details of virusHost category: VERTEBRATES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Aves
Buffer solutionName: GP buffer with 250 mM L-arginine / pH: 10.7 / Details: GP buffer with 250 mM L-arginine
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 K / Details: APV / Method: 3 second blot

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: 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 X / Calibrated magnification: 39000 X / Nominal defocus max: 4900 nm / Nominal defocus min: 500 nm
Astigmatism: astigmatism was corrected at 59,000 times magnification
Camera length: 0 mm
Specimen holderModel: GATAN LIQUID NITROGEN
Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder
Temperature: 90 K / Temperature (max): 95 K / Temperature (min): 88 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
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 (icosahedral)
3D reconstructionMethod: Fourier Bessel / Resolution: 11.3 Å / Num. of particles: 5338 / Nominal pixel size: 1.63 Å / Actual pixel size: 1.57 Å
Magnification calibration: against simian virus 40 atomic coordinates
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: cross-correlation coefficient / Details: METHOD--rigid body REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 1SIE
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 0 0 2004

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