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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 A resolution / Single particle / Vitreous ice (cryo EM))
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

DateDeposition: Apr 19, 2010 / Release: Jan 26, 2011 / Last modification: Mar 9, 2011

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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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)224,6986
Polyers224,6986
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)13,481,893360
Polyers13,481,893360
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)1,123,49130
Polyers1,123,49130
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)1,348,18936
Polyers1,348,18936
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • 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


Mass: 37449.703 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: avian polyomavirus / Aggregation state: PARTICLE / Details: Cryo-EM single particle reconstruction
Details of the virusVirus host category: vertebrates / Virus host species: avian / Virus isolate: SPECIES / Virus type: virion
Buffer solutionName: GP buffer with 250 mM L-arginine
Sample preparationpH: 10.7
Specimen supportDetails: avian polyomavirus in holey carbon grid
VitrificationInstrument: FEI vitrobot / Cryogen name: ETHANE / Temp: 4 K / Humidity: 100% / Details: APV / Method: 3 second blot

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Electron microscopy imaging

EM imagingCamera length: 0 mm
MicroscopyDate: Apr 23, 2007
Electron gunAccelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / 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
Specimen holderSpecimen holder model: 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 deg. / Tilt angle min: 0 deg.
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: UCSF Chimera
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionMethod: Fourier Bessel / Software: PFT3DR / Resolution: 11.3 A / Number of particles: 5338 / Nominal pixel size: 1.63 A/pix / Actual pixel size: 1.57 A/pix
Magnification calibration: against simian virus 40 atomic coordinates
CTF correction method: full CTF correction (FSC cutoff 0.3) / Number of class averages: 0
Atomic model buildingMethod: rigid body / Software name: UCSF Chimera / Ref protocol: rigid body / 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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