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- EMDB-1459: Partitivirus structure reveals a 120-subunit, helix-rich capsid w... -

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Basic information

Entry
Database: EMDB / ID: EMD-1459
TitlePartitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers.
Map dataThis is the final map calculated
Sample
  • Sample: PsV-S
  • Virus: Penicillium stoloniferum virus S
Biological speciesPenicillium stoloniferum virus S
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsOchoa WF / Havens WM / Sinkovits RS / Nibert ML / Ghabrial SA / Baker TS
CitationJournal: Structure / Year: 2008
Title: Partitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers.
Authors: Wendy F Ochoa / Wendy M Havens / Robert S Sinkovits / Max L Nibert / Said A Ghabrial / Timothy S Baker /
Abstract: Two distinct partitiviruses, Penicillium stoloniferum viruses S and F, can be isolated from the fungus Penicillium stoloniferum. The bisegmented dsRNA genomes of these viruses are separately packaged ...Two distinct partitiviruses, Penicillium stoloniferum viruses S and F, can be isolated from the fungus Penicillium stoloniferum. The bisegmented dsRNA genomes of these viruses are separately packaged in icosahedral capsids containing 120 coat-protein subunits. We used transmission electron cryomicroscopy and three-dimensional image reconstruction to determine the structure of Penicillium stoloniferum virus S at 7.3 A resolution. The capsid, approximately 350 A in outer diameter, contains 12 pentons, each of which is topped by five arched protrusions. Each of these protrusions is, in turn, formed by a quasisymmetric dimer of coat protein, for a total of 60 such dimers per particle. The density map shows numerous tubular features, characteristic of alpha helices and consistent with secondary structure predictions for the coat protein. This three-dimensional structure of a virus from the family Partitiviridae exhibits both similarities to and differences from the so-called "T = 2" capsids of other dsRNA viruses.
History
DepositionOct 15, 2007-
Header (metadata) releaseNov 14, 2007-
Map releaseJan 3, 2008-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1459.gif

Downloads & links

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Map

FileDownload / File: emd_1459.map.gz / Format: CCP4 / Size: 206 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the final map calculated
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 381 pix.
= 468.63 Å		1.23 Å/pix.
x 381 pix.
= 468.63 Å		1.23 Å/pix.
x 381 pix.
= 468.63 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.18 / Movie #1: 2.4
Minimum - Maximum-1.77061069 - 6.65659952
Average (Standard dev.)0.23081067 (±0.8776772)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-190-190-190
Dimensions381381381
Spacing381381381
CellA=B=C: 468.63 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z381381381
origin x/y/z0.0000.0000.000
length x/y/z468.630468.630468.630
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS-190-190-190
NC/NR/NS381381381
D min/max/mean-1.7716.6570.231

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Supplemental data

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Sample components

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Entire : PsV-S

EntireName: PsV-S
Components
  • Sample: PsV-S
  • Virus: Penicillium stoloniferum virus S

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Supramolecule #1000: PsV-S

SupramoleculeName: PsV-S / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Penicillium stoloniferum virus S

SupramoleculeName: Penicillium stoloniferum virus S / type: virus / ID: 1 / Name.synonym: PsV-S / NCBI-ID: 216371 / Sci species name: Penicillium stoloniferum virus S / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: PsV-S
Host (natural)Organism: Penicillium Stoloniferum (fungus) / synonym: FUNGI
Virus shellShell ID: 1 / Name: PsV-S / Diameter: 35 Å / T number (triangulation number): 2

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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

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Electron microscopy

MicroscopeFEI TECNAI SPHERA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER
Sample stageSpecimen holder: Polara / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.5 CUT-OFF

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