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

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Basic information

Entry
Database: PDB / ID: 3iym
TitleBackbone Trace of the Capsid Protein Dimer of a Fungal Partitivirus from Electron Cryomicroscopy and Homology Modeling
ComponentsCapsid proteinCapsid
KeywordsVIRUS / dsRNA virus / icosahedral virus / partitivirus / Penicillium stoloniferum virus S / PsV-S
Function / homologyCapsid protein
Function and homology information
Biological speciesPenicillium stoloniferum virus S
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
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.
CitationJournal: Biophys J / Year: 2010
Title: Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling.
Authors: 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 /
Abstract: Most dsRNA viruses have a genome-enclosing capsid that comprises 120 copies of a single coat protein (CP). These 120 CP subunits are arranged as asymmetrical dimers that surround the icosahedral ...Most dsRNA viruses have a genome-enclosing capsid that comprises 120 copies of a single coat protein (CP). These 120 CP subunits are arranged as asymmetrical dimers that surround the icosahedral fivefold axes, forming pentamers of dimers that are thought to be assembly intermediates. This scheme is violated, however, in recent structures of two dsRNA viruses, a fungal virus from family Partitiviridae and a rabbit virus from family Picobirnaviridae, both of which have 120 CP subunits organized as dimers of quasisymmetrical dimers. In this study, we report the CP backbone trace of a second fungal partitivirus, determined in this case by electron cryomicroscopy and homology modeling. This virus also exhibits quasisymmetrical CP dimers that are connected by prominent surface arches and stabilized by domain swapping between the two CP subunits. The CP fold is dominated by alpha-helices, although beta-strands mediate several important contacts. A dimer-of-dimers assembly intermediate is again implicated. The disordered N-terminal tail of each CP subunit protrudes into the particle interior and likely interacts with the genome during packaging and/or transcription. These results broaden our understanding of conserved and variable aspects of partitivirus structure and reflect the growing use of electron cryomicroscopy for atomic modeling of protein folds.
History
DepositionFeb 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2013Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Aug 22, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)93,6612
Polymers93,6612
Non-polymers00
Water0
1
A: Capsid protein
B: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,619,660120
Polymers5,619,660120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
B: Capsid protein
x 5


  • icosahedral pentamer
  • 468 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)468,30510
Polymers468,30510
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
Polymers561,96612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein / Capsid


Mass: 46830.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: virus / Source: (natural) Penicillium stoloniferum virus S / Strain: Penicillium stoloniferum virus S / References: UniProt: Q6YDQ6

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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: PsV-S / Type: VIRUS / Details: authentic virus particles
Details of virusEmpty: NO / Enveloped: NO / Host category: FUNGI / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Penicillium stoloniferum
Buffer solutionName: 50mM Tris pH7.6, 150mM NaCl, 5mM EDTA, 1mM DTT / pH: 7.6 / Details: 50mM Tris pH7.6, 150mM NaCl, 5mM EDTA, 1mM DTT
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

MicroscopyModel: FEI TECNAI 20 / Date: Oct 2, 2006
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / 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 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: Auto3DEM / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.7 Å / Num. of particles: 14252 / Nominal pixel size: 1.27 Å / Actual pixel size: 1.27 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 0 0 3168

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