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- EMDB-1610: 7.5 Amstrong resolution cryo-electron microscopy reconstruction o... -

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Basic information

Entry
Database: EMDB / ID: EMD-1610
Title7.5 Amstrong resolution cryo-electron microscopy reconstruction of Penicillium chrysogenum virus (PcV)
Map dataDensity map of Penicillium chrysogenum virus (PcV)full capsid
Sample
  • Sample: Penicillium chrysogenum virus (PcV) full particles
  • Virus: Penicillium chrysogenum virus
KeywordsPcV / dsRNA viruses / T2 capsid / structural duplication / full capsid
Biological speciesPenicillium chrysogenum virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 7.5 Å
AuthorsLuque D / Gonzalez JM / Garriga D / Ghabrial SA / Trus B / Verdaguer N / Carrascosa JL / Caston JR
CitationJournal: J Virol / Year: 2010
Title: The T=1 capsid protein of Penicillium chrysogenum virus is formed by a repeated helix-rich core indicative of gene duplication.
Authors: Daniel Luque / José M González / Damiá Garriga / Said A Ghabrial / Wendy M Havens / Benes Trus / Nuria Verdaguer / José L Carrascosa / José R Castón /
Abstract: Penicillium chrysogenum virus (PcV), a member of the Chrysoviridae family, is a double-stranded RNA (dsRNA) fungal virus with a multipartite genome, with each RNA molecule encapsidated in a separate ...Penicillium chrysogenum virus (PcV), a member of the Chrysoviridae family, is a double-stranded RNA (dsRNA) fungal virus with a multipartite genome, with each RNA molecule encapsidated in a separate particle. Chrysoviruses lack an extracellular route and are transmitted during sporogenesis and cell fusion. The PcV capsid, based on a T=1 lattice containing 60 subunits of the 982-amino-acid capsid protein, remains structurally undisturbed throughout the viral cycle, participates in genome metabolism, and isolates the virus genome from host defense mechanisms. Using three-dimensional cryoelectron microscopy, we determined the structure of the PcV virion at 8.0 A resolution. The capsid protein has a high content of rod-like densities characteristic of alpha-helices, forming a repeated alpha-helical core indicative of gene duplication. Whereas the PcV capsid protein has two motifs with the same fold, most dsRNA virus capsid subunits consist of dimers of a single protein with similar folds. The spatial arrangement of the alpha-helical core resembles that found in the capsid protein of the L-A virus, a fungal totivirus with an undivided genome, suggesting a conserved basic fold. The encapsidated genome is organized in concentric shells; whereas the inner dsRNA shells are well defined, the outermost layer is dense due to numerous interactions with the inner capsid surface, specifically, six interacting areas per monomer. The outermost genome layer is arranged in an icosahedral cage, sufficiently well ordered to allow for modeling of an A-form dsRNA. The genome ordering might constitute a framework for dsRNA transcription at the capsid interior and/or have a structural role for capsid stability.
History
DepositionMar 26, 2009-
Header (metadata) releaseApr 15, 2009-
Map releaseNov 15, 2010-
UpdateDec 26, 2012-
Current statusDec 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1610.png

Downloads & links

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Map

FileDownload / File: emd_1610.map.gz / Format: CCP4 / Size: 147.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of Penicillium chrysogenum virus (PcV)full capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 341 pix.
= 477.4 Å		1.4 Å/pix.
x 341 pix.
= 477.4 Å		1.4 Å/pix.
x 341 pix.
= 477.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-1.62926 - 3.75725
Average (Standard dev.)0.186445 (±0.457735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions341341341
Spacing341341341
CellA=B=C: 477.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z341341341
origin x/y/z0.0000.0000.000
length x/y/z477.400477.400477.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS341341341
D min/max/mean-1.6293.7570.186

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Supplemental data

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Segmentation: Penicillium chrysogenum virus (PcV) capsid subunit mask

AnnotationPenicillium chrysogenum virus (PcV) capsid subunit mask
Fileemd_1610_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Penicillium chrysogenum virus (PcV) full particles

EntireName: Penicillium chrysogenum virus (PcV) full particles
Components
  • Sample: Penicillium chrysogenum virus (PcV) full particles
  • Virus: Penicillium chrysogenum virus

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Supramolecule #1000: Penicillium chrysogenum virus (PcV) full particles

SupramoleculeName: Penicillium chrysogenum virus (PcV) full particles / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 6.5 MDa

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Supramolecule #1: Penicillium chrysogenum virus

SupramoleculeName: Penicillium chrysogenum virus / type: virus / ID: 1 / Name.synonym: PcV / NCBI-ID: 158372 / Sci species name: Penicillium chrysogenum virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: PcV
Host (natural)Organism: Penicillium chrysogenum (fungus) / synonym: FUNGI
Virus shellShell ID: 1 / Name: CP / Diameter: 400 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8 / Details: 50 mM Tris-HCl pH 7.8, 5 mM EDTA,150 mM NaCl
StainingType: NEGATIVE
Details: Samples of empty- and full-enriched particles fractions were applied to one side of a holey carbon grid, blotted and plunged into liquid ethane
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 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
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 56 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: PFT2 EM3DR2 / Number images used: 4156

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