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- EMDB-1301: Electron cryomicroscopy comparison of the architectures of the en... -

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Basic information

Entry
Database: EMDB / ID: EMD-1301
TitleElectron cryomicroscopy comparison of the architectures of the enveloped bacteriophages phi6 and phi8.
Map data3D reconstruction of the bacteriophage Phi6 virion.
Sample
  • Sample: Bacteriophage Phi6 virion
  • Virus: Pseudomonas phage phi6 (bacteriophage)
Biological speciesPseudomonas phage phi6 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsJaalinoja HT / Huiskonen JT / Butcher SJ
CitationJournal: Structure / Year: 2007
Title: Electron cryomicroscopy comparison of the architectures of the enveloped bacteriophages phi6 and phi8.
Authors: Harri T Jäälinoja / Juha T Huiskonen / Sarah J Butcher /
Abstract: The enveloped dsRNA bacteriophages phi6 and phi8 are the two most distantly related members of the Cystoviridae family. Their structure and function are similar to that of the Reoviridae but their ...The enveloped dsRNA bacteriophages phi6 and phi8 are the two most distantly related members of the Cystoviridae family. Their structure and function are similar to that of the Reoviridae but their assembly can be conveniently studied in vitro. Electron cryomicroscopy and three-dimensional icosahedral reconstruction were used to determine the structures of the phi6 virion (14 A resolution), phi8 virion (18 A resolution), and phi8 core (8.5 A resolution). Spikes protrude 2 nm from the membrane bilayer in phi6 and 7 nm in phi8. In the phi6 nucleocapsid, 600 copies of P8 and 72 copies of P4 interact with the membrane, whereas in phi8 it is only P4 and 60 copies of a minor protein. The major polymerase complex protein P1 forms a dodecahedral shell from 60 asymmetric dimers in both viruses, but the alpha-helical fold has apparently diverged. These structural differences reflect the different host ranges and entry and assembly mechanisms of the two viruses.
History
DepositionNov 27, 2006-
Header (metadata) releaseNov 27, 2006-
Map releaseMar 19, 2007-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1290
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1290
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1301.map.gz / Format: CCP4 / Size: 127.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of the bacteriophage Phi6 virion.
Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level1: 1700.0 / Movie #1: 1290
Minimum - Maximum-3767.139999999999873 - 4292.260000000000218
Average (Standard dev.)-0.000000164804 (±680.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-324-324-324
Dimensions325325325
Spacing325325325
CellA=B=C: 910 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z325325325
origin x/y/z0.0000.0000.000
length x/y/z910.000910.000910.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-324-324-324
NC/NR/NS325325325
D min/max/mean-3767.1394292.262-0.000

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Supplemental data

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Sample components

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Entire : Bacteriophage Phi6 virion

EntireName: Bacteriophage Phi6 virion
Components
  • Sample: Bacteriophage Phi6 virion
  • Virus: Pseudomonas phage phi6 (bacteriophage)

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Supramolecule #1000: Bacteriophage Phi6 virion

SupramoleculeName: Bacteriophage Phi6 virion / type: sample / ID: 1000 / Oligomeric state: complete virion / Number unique components: 1

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Supramolecule #1: Pseudomonas phage phi6

SupramoleculeName: Pseudomonas phage phi6 / type: virus / ID: 1 / Name.synonym: Cystovirus Phi6 virion / NCBI-ID: 10879 / Sci species name: Pseudomonas phage phi6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: Cystovirus Phi6 virion
Host (natural)Organism: Pseudomonads syringae / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: Nucleocapsid / Diameter: 550 Å / T number (triangulation number): 13

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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

BufferDetails: 10 mM potassium phosphate pH 7.5, 1 mM MgCl2
GridDetails: 400 mesh copper grid, Quantifoil R2/2 holey
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: EMBL design
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 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 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off excess buffer, sufficient to leave a thin layer on the grid. 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 in liquid nitrogen for later use in the microscope.

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49300 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 90 K / Max: 94 K / Average: 93 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 23 / Details: The data was processed at 2.8 ??/pixel sampling. / Bits/pixel: 12
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle, wiener factor 0.1
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: pft2, em3dr2, POR, P3DR / Number images used: 517

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