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- PDB-3iym: Backbone Trace of the Capsid Protein Dimer of a Fungal Partitivir... -

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Entry
Database: PDB / ID: 3iym
TitleBackbone Trace of the Capsid Protein Dimer of a Fungal Partitivirus from Electron Cryomicroscopy and Homology Modeling
DescriptorCapsid protein
KeywordsVIRUS / dsRNA virus / icosahedral virus / partitivirus / Penicillium stoloniferum virus S / PsV-S
Specimen sourcePenicillium stoloniferum virus S / virus
MethodElectron microscopy (4.7 Å resolution / Particle / Single particle)
AuthorsTang, J. / Pan, J. / Havens, W.F. / Ochoa, W.F. / Li, H. / Sinkovits, R.S. / Guu, T.S.Y. / Ghabrial, S.A. / Nibert, M.L. / Tao, J.Y. / Baker, T.S.
CitationBiophys. J., 2010, 99, 685-694

Biophys. J., 2010, 99, 685-694 StrPapers
Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling.
Jinghua Tang / Junhua Pan / Wendy M Havens / Wendy F Ochoa / Tom S Y Guu / Said A Ghabrial / Max L Nibert / Yizhi Jane Tao / Timothy S Baker

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 5, 2010 / Release: Jul 28, 2010
RevisionDateData content typeGroupProviderType
1.0Jul 28, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Nov 13, 2013Structure modelOther

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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
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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)93,6612
Polyers93,6612
Non-polymers00
Water0
#1
A: Capsid protein
B: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,619,660120
Polyers5,619,660120
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: Capsid protein
B: Capsid protein
x 5


  • icosahedral pentamer
  • 468 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)468,30510
Polyers468,30510
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: Capsid protein
B: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 562 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)561,96612
Polyers561,96612
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)Capsid protein


Mass: 46830.504 Da / Num. of mol.: 2 / Source: (natural) Penicillium stoloniferum virus S / virus / References: UniProt: Q6YDQ6

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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: PsV-S / Type: VIRUS / Details: authentic virus particles
Details of virusEmpty: NO / Enveloped: NO / Virus host category: FUNGI / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Penicillium stoloniferum
Buffer solutionName: 50mM Tris pH7.6, 150mM NaCl, 5mM EDTA, 1mM DTT / Details: 50mM Tris pH7.6, 150mM NaCl, 5mM EDTA, 1mM DTT / pH: 7.6
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 89 K / Humidity: 80 % / Method: blot for 7.5 seconds before plunging

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI 20 / Date: Oct 2, 2006
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Nominal defocus max: 2.2 nm / Nominal defocus min: 1.4 nm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Eucentric / Temperature: 77 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: Auto3dem / Category: RECONSTRUCTION
SymmetryPoint symmetry: I
3D reconstructionResolution: 4.7 Å / Number of particles: 14252 / Nominal pixel size: 1.27 / Actual pixel size: 1.27 / Symmetry type: POINT
Number of atoms included #LASTProtein: 3168 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3168

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