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- EMDB-5171: Structure of Fusarium poae virus 1 shows conserved and variable e... -

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Basic information

Entry
Database: EMDB / ID: EMD-5171
TitleStructure of Fusarium poae virus 1 shows conserved and variable elements of partitivirus capsids and evolutionary links to picobirnaviruses
Map datamap of fpv1
Sample
  • Sample: fpv1
  • Virus: fpv1 (unknown)
KeywordsCapsid protein Cryoelectron microscopy dsRNA virus Electron cryomicroscopy Fungal virus Virus structure
Biological speciesfpv1 (unknown)
Methodsingle particle reconstruction / cryo EM
AuthorsTang J / Ochoa WF / Li H / Havens WM / Nibert ML / Ghabrial SA / Baker TS
CitationJournal: J Struct Biol / Year: 2010
Title: Structure of Fusarium poae virus 1 shows conserved and variable elements of partitivirus capsids and evolutionary relationships to picobirnavirus.
Authors: Jinghua Tang / Wendy F Ochoa / Hua Li / Wendy M Havens / Max L Nibert / Said A Ghabrial / Timothy S Baker /
Abstract: Filamentous fungus Fusarium poae is a worldwide cause of the economically important disease Fusarium head blight of cereal grains. The fungus is itself commonly infected with a bisegmented dsRNA ...Filamentous fungus Fusarium poae is a worldwide cause of the economically important disease Fusarium head blight of cereal grains. The fungus is itself commonly infected with a bisegmented dsRNA virus from the family Partitiviridae. For this study, we determined the structure of partitivirus Fusarium poae virus 1 (FpV1) to a resolution of 5.6Å or better by electron cryomicroscopy and three-dimensional image reconstruction. The main structural features of FpV1 are consistent with those of two other fungal partitiviruses for which high-resolution structures have been recently reported. These shared features include a 120-subunit T=1 capsid comprising 60 quasisymmetrical capsid protein dimers with both shell and protruding domains. Distinguishing features are evident throughout the FpV1 capsid, however, consistent with its more massive subunits and its greater phylogenetic divergence relative to the other two structurally characterized partitiviruses. These results broaden our understanding of conserved and variable elements of fungal partitivirus structure, as well as that of vertebrate picobirnavirus, and support the suggestion that a phylogenetic subcluster of partitiviruses closely related to FpV1 should constitute a separate taxonomic genus.
History
DepositionMar 9, 2010-
Header (metadata) releaseApr 15, 2010-
Map releaseNov 17, 2010-
UpdateAug 1, 2011-
Current statusAug 1, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5171.map.gz / Format: CCP4 / Size: 74.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of fpv1
Voxel sizeX=Y=Z: 1.95 Å
Density
Contour LevelBy EMDB: 2.1 / Movie #1: 1
Minimum - Maximum-6.38511 - 10.187799999999999
Average (Standard dev.)0.00000000393396 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-135-135-135
Dimensions271271271
Spacing271271271
CellA=B=C: 528.45 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.951.951.95
M x/y/z271271271
origin x/y/z0.0000.0000.000
length x/y/z528.450528.450528.450
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-135-135-135
NC/NR/NS271271271
D min/max/mean-6.38510.1880.000

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Supplemental data

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Sample components

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Entire : fpv1

EntireName: fpv1
Components
  • Sample: fpv1
  • Virus: fpv1 (unknown)

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Supramolecule #1000: fpv1

SupramoleculeName: fpv1 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: fpv1

SupramoleculeName: fpv1 / type: virus / ID: 1 / Name.synonym: fpv1 / Sci species name: fpv1 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: fpv1
Host (natural)Organism: Fungi (eukaryote) / synonym: FUNGI
Virus shellShell ID: 1 / Diameter: 420 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
DateJul 21, 2006
Image recordingDigitization - Sampling interval: 1.95 µm / Number real images: 240
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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