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- EMDB-5161: PsV-F -

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Basic information

Entry
Database: EMDB / ID: EMD-5161
TitlePsV-F
Map dataPsV-F
Sample
  • Sample: PsV-F
  • Virus: Penicillium stoloniferum virus F
Keywordsde nova modeling / dsRNA virus
Function / homology: / PsV, capsid protein / Capsid protein
Function and homology information
Biological speciesPenicillium stoloniferum virus F
Methodsingle particle reconstruction / cryo EM
AuthorsTang J / Pan J / Havens WM / Ochoa WF / Li H / Sinkovits RS / Guu TSY / Ghabrial SA / Nibert ML / Tao YJ / Baker TS
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
DepositionJan 29, 2010-
Header (metadata) releaseFeb 17, 2010-
Map releaseAug 12, 2010-
UpdateNov 2, 2010-
Current statusNov 2, 2010Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3iym
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iym
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Structure viewerEM map:
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Supplemental images

emd_5161_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5161.map.gz / Format: CCP4 / Size: 116.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPsV-F
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 315 pix.
= 313.82 Å		1.42 Å/pix.
x 315 pix.
= 313.82 Å		1.42 Å/pix.
x 315 pix.
= 313.82 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-4.36001 - 8.21834
Average (Standard dev.)0.00000000314616 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-157-157-157
Dimensions315315315
Spacing315315315
CellA=B=C: 313.82 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z221221221
origin x/y/z0.0000.0000.000
length x/y/z313.820313.820313.820
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-157-157-157
NC/NR/NS315315315
D min/max/mean-4.3608.2180.000

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Supplemental data

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Sample components

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Entire : PsV-F

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

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Supramolecule #1000: PsV-F

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

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Supramolecule #1: Penicillium stoloniferum virus F

SupramoleculeName: Penicillium stoloniferum virus F / type: virus / ID: 1 / Name.synonym: PsV-F / NCBI-ID: 296210 / Sci species name: Penicillium stoloniferum virus F / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: PsV-F
Host (natural)Organism: Fungi (eukaryote) / synonym: FUNGI
Virus shellShell ID: 1 / Diameter: 380 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 / Details: Vitrification instrument: vitrobot / Method: freezing with vitrobot for 4 second

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Electron microscopy

MicroscopeFEI POLARA 300
DetailsLow dose microscopy with LEGINON at 105K magnification
DateOct 2, 2006
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Number real images: 193
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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