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- EMDB-1300: Electron cryomicroscopy comparison of the architectures of the en... -

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Basic information

Entry
Database: EMDB / ID: EMD-1300
TitleElectron cryomicroscopy comparison of the architectures of the enveloped bacteriophages phi6 and phi8.
Map data3D reconstruction of the bacteriophage Phi8 polymerase complex
Sample
  • Sample: Bacteriophage Phi8 core
  • Virus: Pseudomonas phage phi8 (bacteriophage)
Function / homology: / Major inner capsid protein P1 / identical protein binding / p1
Function and homology information
Biological speciesPseudomonas phage phi8 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 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-
UpdateSep 18, 2013-
Current statusSep 18, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5500
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5500
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4bx4
  • Surface level: 17000
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4bx4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1300.gif

Downloads & links

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Map

FileDownload / File: emd_1300.map.gz / Format: CCP4 / Size: 298.2 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotation3D reconstruction of the bacteriophage Phi8 polymerase complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 543 pix.
= 760.2 Å		1.4 Å/pix.
x 543 pix.
= 760.2 Å		1.4 Å/pix.
x 543 pix.
= 760.2 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 Level1: 10400.0 / Movie #1: 5500
Minimum - Maximum-16403.0 - 32443.0
Average (Standard dev.)289.648000000000025 (±4869.329999999999927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions543543543
Spacing543543543
CellA=B=C: 760.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.41.41.4
M x/y/z543543543
origin x/y/z0.0000.0000.000
length x/y/z760.200760.200760.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS543543543
D min/max/mean-16403.00032443.000289.648

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Supplemental data

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Segmentation: Subunit A

AnnotationSubunit A
Fileemd_1300_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Segmentation: Subunit A

AnnotationSubunit A
Fileemd_1300_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Others

Details[MASK_details.txt]
mask_phi8_subunitA_emd1300.map> emd_1300_msk_1.map
mask_phi8_subunitB_emd1300.map> emd_1300_msk_2.map

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Sample components

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Entire : Bacteriophage Phi8 core

EntireName: Bacteriophage Phi8 core
Components
  • Sample: Bacteriophage Phi8 core
  • Virus: Pseudomonas phage phi8 (bacteriophage)

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Supramolecule #1000: Bacteriophage Phi8 core

SupramoleculeName: Bacteriophage Phi8 core / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Pseudomonas phage phi8

SupramoleculeName: Pseudomonas phage phi8 / type: virus / ID: 1 / Name.synonym: Cystovirus Phi8 polymerase complex / NCBI-ID: 120086 / Sci species name: Pseudomonas phage phi8 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: Cystovirus Phi8 polymerase complex
Host (natural)Organism: Pseudomonads syringae / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: Polymerase complex / Diameter: 500 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

BufferDetails: 10 mM potassium phosphate pH7.5, 1 mM MgCl2, 50 mM NaCl
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: 3.3 µm / Nominal defocus min: 0.7 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: 66 / 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: 8.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: pft2, em3dr2, POR, P3DR / Number images used: 12867

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