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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
DescriptorMajor capsid protein VP1
KeywordsVIRUS / avian / polyomavirus / APV / icosahedral virus
Specimen sourceBudgerigar fledgling disease polyomavirus / virus / BFPyV / セキセイインコヒナ病ポリオーマウイルス
MethodElectron microscopy (11.3 Å resolution / Particle / Single particle)
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.
CitationVirology, 2011, 411, 142-152

Virology, 2011, 411, 142-152 StrPapers
The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4.
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 19, 2010 / Release: Jan 26, 2011
RevisionDateData content typeGroupProviderType
1.0Jan 26, 2011Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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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
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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: Polypeptide(L)
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 / virus / セキセイインコヒナ病ポリオーマウイルス
References: UniProt: P13891

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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 FIELD / 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
2PFT3DRRECONSTRUCTION
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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