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- EMDB-1597: 5-fold averaged density map of Paramecium bursaria Chlorella viru... -

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Basic information

Entry
Database: EMDB / ID: EMD-1597
Title5-fold averaged density map of Paramecium bursaria Chlorella virus-1 (PBCV-1).
Map data5-fold average density map of Paramecium bursaria Chlorella virus-1 (PBCV-1).
Sample
  • Sample: Paramecium bursaria Chlorella virus-1 (PBCV-1)
  • Virus: Paramecium bursaria Chlorella virus 1
KeywordsPBCV-1 / eukaryotic virus / tail / pocket / 5-fold averaged
Biological speciesParamecium bursaria Chlorella virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsCherrier MV / Kostyuchenko VA / Xiao C / Bowman VD / Battisti AJ / Yan X / Chipman PR / Baker TS / Van Etten JL / Rossmann MG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: An icosahedral algal virus has a complex unique vertex decorated by a spike.
Authors: Mickaël V Cherrier / Victor A Kostyuchenko / Chuan Xiao / Valorie D Bowman / Anthony J Battisti / Xiaodong Yan / Paul R Chipman / Timothy S Baker / James L Van Etten / Michael G Rossmann /
Abstract: Paramecium bursaria Chlorella virus-1 is an icosahedrally shaped, 1,900-A-diameter virus that infects unicellular eukaryotic green algae. A 5-fold symmetric, 3D reconstruction using cryoelectron ...Paramecium bursaria Chlorella virus-1 is an icosahedrally shaped, 1,900-A-diameter virus that infects unicellular eukaryotic green algae. A 5-fold symmetric, 3D reconstruction using cryoelectron microscopy images has now shown that the quasiicosahedral virus has a unique vertex, with a pocket on the inside and a spike structure on the outside of the capsid. The pocket might contain enzymes for use in the initial stages of infection. The unique vertex consists of virally coded proteins, some of which have been identified. Comparison of shape, size, and location of the spike with similar features in bacteriophages T4 and P22 suggests that the spike might be a cell-puncturing device. Similar asymmetric features may have been missed in previous analyses of many other viruses that had been assumed to be perfectly icosahedral.
History
DepositionApr 13, 2009-
Header (metadata) releaseApr 21, 2009-
Map releaseJun 4, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

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

EMD-1597-ima...

Downloads & links

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Map

FileDownload / File: emd_1597.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation5-fold average density map of Paramecium bursaria Chlorella virus-1 (PBCV-1).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8 Å/pix.
x 360 pix.
= 2880. Å		8 Å/pix.
x 360 pix.
= 2880. Å		8 Å/pix.
x 360 pix.
= 2880. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.5 / Movie #1: 1
Minimum - Maximum-13.7163 - 16.923300000000001
Average (Standard dev.)-0.00383085 (±1.0004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 2880 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z888
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z2880.0002880.0002880.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-13.71616.923-0.004

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Supplemental data

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Sample components

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Entire : Paramecium bursaria Chlorella virus-1 (PBCV-1)

EntireName: Paramecium bursaria Chlorella virus-1 (PBCV-1)
Components
  • Sample: Paramecium bursaria Chlorella virus-1 (PBCV-1)
  • Virus: Paramecium bursaria Chlorella virus 1

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Supramolecule #1000: Paramecium bursaria Chlorella virus-1 (PBCV-1)

SupramoleculeName: Paramecium bursaria Chlorella virus-1 (PBCV-1) / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Paramecium bursaria Chlorella virus 1

SupramoleculeName: Paramecium bursaria Chlorella virus 1 / type: virus / ID: 1 / Name.synonym: PBCV-1 / NCBI-ID: 10506 / Sci species name: Paramecium bursaria Chlorella virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: PBCV-1
Host (natural)Organism: Chlorella NC64A / synonym: ALGAE
Virus shellShell ID: 1 / Name: VP54 / Diameter: 1900 Å

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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: HOMEMADE PLUNGER
Details: Vitrification instrument: Guillotine-style plunge freezing device
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 98 K
Alignment procedureLegacy - Electron beam tilt params: 0
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 228 / Average electron dose: 22 e/Å2
Details: All particles were scaled to 4.0A per pixel, then bin twice to 8.0A per pixel.
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.473 µm / Nominal defocus min: 1.302 µm / Nominal magnification: 38000
Sample stageSpecimen holder: EUCENTRIC / Specimen holder model: GATAN LIQUID NITROGEN

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Electron microscopy #2

Microscopy ID2
MicroscopeFEI/PHILIPS CM300FEG/T
TemperatureAverage: 98 K
Alignment procedureLegacy - Astigmatism: live FFT / Legacy - Electron beam tilt params: 0
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 228 / Average electron dose: 24 e/Å2
Details: All particles were scaled to 4.0A per pixel, then bin twice to 8.0A per pixel.
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.728 µm / Nominal defocus min: 0.767 µm / Nominal magnification: 45000
Sample stageSpecimen holder: EUCENTRIC / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider, XMIPP / Details: The 3D map was only 5 fold averaged. / Number images used: 5149

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