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- EMDB-5384: The structure of PBCV-1 (five-fold averaged map) -

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Basic information

Entry
Database: EMDB / ID: EMD-5384
TitleThe structure of PBCV-1 (five-fold averaged map)
Map dataFive-fold averaged map of PBCV-1
Sample
  • Sample: PBCV-1
  • Virus: Paramecium bursaria Chlorella virus 1
KeywordsCell entry / minor protein / double jelly-roll
Biological speciesParamecium bursaria Chlorella virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 9.8 Å
AuthorsZhang XZ / Xiang Y / Dunigan DD / Klose T / Chipman PR / Etten JLV / Rossmann MG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Three-dimensional structure and function of the Paramecium bursaria chlorella virus capsid.
Authors: Xinzheng Zhang / Ye Xiang / David D Dunigan / Thomas Klose / Paul R Chipman / James L Van Etten / Michael G Rossmann /
Abstract: A cryoelectron microscopy 8.5 Å resolution map of the 1,900 Å diameter, icosahedral, internally enveloped Paramecium bursaria chlorella virus was used to interpret structures of the virus at ...A cryoelectron microscopy 8.5 Å resolution map of the 1,900 Å diameter, icosahedral, internally enveloped Paramecium bursaria chlorella virus was used to interpret structures of the virus at initial stages of cell infection. A fivefold averaged map demonstrated that two minor capsid proteins involved in stabilizing the capsid are missing in the vicinity of the unique vertex. Reconstruction of the virus in the presence of host chlorella cell walls established that the spike at the unique vertex initiates binding to the cell wall, which results in the enveloped nucleocapsid moving closer to the cell. This process is concurrent with the release of the internal viral membrane that was linked to the capsid by many copies of a viral membrane protein in the mature infectous virus. Simultaneously, part of the trisymmetrons around the unique vertex disassemble, probably in part because two minor capsid proteins are absent, causing Paramecium bursaria chlorella virus and the cellular contents to merge, possibly as a result of enzyme(s) within the spike assembly. This may be one of only a few recordings of successive stages of a virus while infecting a eukaryotic host in pseudoatomic detail in three dimensions.
History
DepositionJan 12, 2012-
Header (metadata) releaseJun 28, 2012-
Map releaseJun 28, 2012-
UpdateJun 28, 2012-
Current statusJun 28, 2012Processing 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
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5384_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5384.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFive-fold averaged map of PBCV-1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.84 Å/pix.
x 700 pix.
= 2688. Å		3.84 Å/pix.
x 700 pix.
= 2688. Å		3.84 Å/pix.
x 700 pix.
= 2688. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-8.686364169999999 - 10.981709479999999
Average (Standard dev.)0.00068056 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-350-350-350
Dimensions700700700
Spacing700700700
CellA=B=C: 2688.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.843.843.84
M x/y/z700700700
origin x/y/z0.0000.0000.000
length x/y/z2688.0002688.0002688.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-350-350-350
NC/NR/NS700700700
D min/max/mean-8.68610.9820.001

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Supplemental data

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Sample components

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Entire : PBCV-1

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

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Supramolecule #1000: PBCV-1

SupramoleculeName: PBCV-1 / type: sample / ID: 1000 / Number unique components: 8

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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 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: PBCV-1
Host (natural)Organism: Chlorella variabilis (plant) / synonym: ALGAE
Virus shellShell ID: 1 / Name: VP54 / Diameter: 1850 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

Concentration1 mg/mL
BufferpH: 7 / Details: BBM
GridDetails: 200 mesh grid
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 174 K / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
TemperatureAverage: 175 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 250,000 times magnification
Image recordingCategory: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 6.75 µm / Number real images: 800 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 33065 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder: Single tilt holder / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 17016

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