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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 data
SamplePsV-S:
virus
Biological speciesPenicillium stoloniferum virus S (PsV-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
  • Download
  • 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

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)
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
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 / Number of components: 1

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Component #1: virus, Penicillium stoloniferum virus S

VirusName: Penicillium stoloniferum virus S / a.k.a: PsV-S / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Penicillium stoloniferum virus S (PsV-S)
Source (natural)Host Species: Penicillium Stoloniferum (fungus) / Host category: FUNGI
Shell #1Name of element: PsV-S / Diameter: 35 Å / T number (triangulation number): 2

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI SPHERA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
LensImaging mode: OTHER
Specimen HolderHolder: Polara / Model: GATAN LIQUID NITROGEN

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (正20面体型対称)
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.5

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