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- EMDB-1222: Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals or... -

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Basic information

Entry
Database: EMDB / ID: EMD-1222
TitleCryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery.
Map dataThis is the map of bacteriophage P22.
Sample
  • Sample: Bacteriophage P22
  • Virus: Enterobacteria phage P22 (virus)
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsChang J / Weigele P / King J / Chiu W / Jiang W
CitationJournal: Structure / Year: 2006
Title: Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery.
Authors: Juan Chang / Peter Weigele / Jonathan King / Wah Chiu / Wen Jiang /
Abstract: The mechanisms by which most double-stranded DNA viruses package and release their genomic DNA are not fully understood. Single particle cryo-electron microscopy and asymmetric 3D reconstruction ...The mechanisms by which most double-stranded DNA viruses package and release their genomic DNA are not fully understood. Single particle cryo-electron microscopy and asymmetric 3D reconstruction reveal the organization of the complete bacteriophage P22 virion, including the protein channel through which DNA is first packaged and later ejected. This channel is formed by a dodecamer of portal proteins and sealed by a tail hub consisting of two stacked barrels capped by a protein needle. Six trimeric tailspikes attached around this tail hub are kinked, suggesting a functional hinge that may be used to trigger DNA release. Inside the capsid, the portal's central channel is plugged by densities interpreted as pilot/injection proteins. A short rod-like density near these proteins may be the terminal segment of the dsDNA genome. The coaxially packed DNA genome is encapsidated by the icosahedral shell. This complete structure unifies various biochemical, genetic, and crystallographic data of its components from the past several decades.
History
DepositionMay 9, 2006-
Header (metadata) releaseMay 9, 2006-
Map releaseNov 1, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1222.gif

Downloads & links

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Map

FileDownload / File: emd_1222.map.gz / Format: CCP4 / Size: 89 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the map of bacteriophage P22.
Voxel sizeX=Y=Z: 4.07 Å
Density
Contour Level1: 0.799 / Movie #1: 2.6
Minimum - Maximum-3.98884 - 5.88857
Average (Standard dev.)0.000000000102223 (±0.745929)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-144-144-144
Dimensions288288288
Spacing288288288
CellA=B=C: 1172.16 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.074.074.07
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z1172.1601172.1601172.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-144-144-144
NC/NR/NS288288288
D min/max/mean-3.9895.8890.000

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Supplemental data

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Sample components

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Entire : Bacteriophage P22

EntireName: Bacteriophage P22 (virus)
Components
  • Sample: Bacteriophage P22
  • Virus: Enterobacteria phage P22 (virus)

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Supramolecule #1000: Bacteriophage P22

SupramoleculeName: Bacteriophage P22 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / Name.synonym: P22 / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: P22
Host (natural)Organism: Salmonella (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: gp5 / Diameter: 700 Å / T number (triangulation number): 7

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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

BufferpH: 7.5 / Details: 10 mM Tris pH 7.5, 1mM MgCl2
GridDetails: 200 mesh copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeJEOL 2010F
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Average electron dose: 10 e/Å2

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 16000

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