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- EMDB-1220: The structure of an infectious P22 virion shows the signal for he... -

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Basic information

Entry
Database: EMDB / ID: EMD-1220
TitleThe structure of an infectious P22 virion shows the signal for headful DNA packaging.
Map dataSurface rendered view of the asymmetric P22 Virion
Sample
  • Sample: P22 Bacteriophage Virion
  • Virus: Enterobacteria phage P22 (virus)
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsLander GC / Tang L / Casjens SR / Gilcrease EB / Prevelige P / Poliakov A / Potter CS / Carragher B / Johnson JE
CitationJournal: Science / Year: 2006
Title: The structure of an infectious P22 virion shows the signal for headful DNA packaging.
Authors: Gabriel C Lander / Liang Tang / Sherwood R Casjens / Eddie B Gilcrease / Peter Prevelige / Anton Poliakov / Clinton S Potter / Bridget Carragher / John E Johnson /
Abstract: Bacteriophages, herpesviruses, and other large double-stranded DNA (dsDNA) viruses contain molecular machines that pump DNA into preassembled procapsids, generating internal capsid pressures ...Bacteriophages, herpesviruses, and other large double-stranded DNA (dsDNA) viruses contain molecular machines that pump DNA into preassembled procapsids, generating internal capsid pressures exceeding, by 10-fold, that of bottled champagne. A 17 angstrom resolution asymmetric reconstruction of the infectious P22 virion reveals that tightly spooled DNA about the portal dodecamer forces a conformation that is significantly different from that observed in isolated portals assembled from ectopically expressed protein. We propose that the tight dsDNA spooling activates the switch that signals the headful chromosome packing density to the particle exterior.
History
DepositionMay 4, 2006-
Header (metadata) releaseMay 5, 2006-
Map releaseJun 3, 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: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1220.gif

Downloads & links

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Map

FileDownload / File: emd_1220.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface rendered view of the asymmetric P22 Virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.04 Å/pix.
x 256 pix.
= 1034.24 Å		4.04 Å/pix.
x 256 pix.
= 1034.24 Å		4.04 Å/pix.
x 256 pix.
= 1034.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.04 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.981 / Movie #1: 3
Minimum - Maximum-10.205500000000001 - 13.7524
Average (Standard dev.)0.00943773 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 1034.24 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.044.044.04
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z1034.2401034.2401034.240
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-10.20613.7520.009

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Supplemental data

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Sample components

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Entire : P22 Bacteriophage Virion

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

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Supramolecule #1000: P22 Bacteriophage Virion

SupramoleculeName: P22 Bacteriophage Virion / 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 / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salmonella enterica (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: gp5 / Diameter: 600 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

Concentration10 mg/mL
BufferpH: 7.4 / Details: 10mM Tris-HCL, 1mM MgCl2
GridDetails: Quantifoil 2/2 400 mesh grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4.2 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 4.5 K / Max: 4.8 K / Average: 4.5 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected automatically at 50,000 times magnification
Specialist opticsEnergy filter - Name: FEI / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 25.0 eV
Detailsimages collected automatically with LEGINON
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS / Number real images: 4899 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 80000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 80000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles selected manually, CTF estimation was performed using Automated CTF-Estimation Matlab package (ACE)
CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, EMAN / Number images used: 22968

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