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- EMDB-1420: DNA poised for release in bacteriophage phi29. -

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Basic information

Entry
Database: EMDB / ID: EMD-1420
TitleDNA poised for release in bacteriophage phi29.
Map data3D map of fiberless phi29 virion
Sample
  • Sample: phi29 fiberless virion
  • Virus: Bacillus phage phi29 (virus)
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsTang J / Olson N / Jardine P / Grimes S / Anderson D / Baker T
CitationJournal: Structure / Year: 2008
Title: DNA poised for release in bacteriophage phi29.
Authors: Jinghua Tang / Norman Olson / Paul J Jardine / Shelley Grimes / Dwight L Anderson / Timothy S Baker /
Abstract: We present here the first asymmetric, three-dimensional reconstruction of a tailed dsDNA virus, the mature bacteriophage phi29, at subnanometer resolution. This structure reveals the rich detail of ...We present here the first asymmetric, three-dimensional reconstruction of a tailed dsDNA virus, the mature bacteriophage phi29, at subnanometer resolution. This structure reveals the rich detail of the asymmetric interactions and conformational dynamics of the phi29 protein and DNA components, and provides novel insight into the mechanics of virus assembly. For example, the dodecameric head-tail connector protein undergoes significant rearrangement upon assembly into the virion. Specific interactions occur between the tightly packed dsDNA and the proteins of the head and tail. Of particular interest and novelty, an approximately 60A diameter toroid of dsDNA was observed in the connector-lower collar cavity. The extreme deformation that occurs over a small stretch of DNA is likely a consequence of the high pressure of the packaged genome. This toroid structure may help retain the DNA inside the capsid prior to its injection into the bacterial host.
History
DepositionSep 10, 2007-
Header (metadata) releaseSep 10, 2007-
Map releaseSep 10, 2008-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • 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

1420.gif

Downloads & links

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Map

FileDownload / File: emd_1420.map.gz / Format: CCP4 / Size: 101.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of fiberless phi29 virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.68 Å/pix.
x 301 pix.
= 301.76 Å		3.68 Å/pix.
x 301 pix.
= 301.76 Å		3.68 Å/pix.
x 301 pix.
= 301.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.68 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.27 / Movie #1: 2.5
Minimum - Maximum-0.159463 - 23.732399999999998
Average (Standard dev.)0.00000000790474 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-105
Dimensions301301301
Spacing301301301
CellA=B=C: 301.76 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.683.683.68
M x/y/z828282
origin x/y/z0.0000.0000.000
length x/y/z301.760301.760301.760
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-30-49
NX/NY/NZ6060100
MAP C/R/S123
start NC/NR/NS-150-150-105
NC/NR/NS301301301
D min/max/mean-0.15923.7320.000

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Supplemental data

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Sample components

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Entire : phi29 fiberless virion

EntireName: phi29 fiberless virion
Components
  • Sample: phi29 fiberless virion
  • Virus: Bacillus phage phi29 (virus)

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Supramolecule #1000: phi29 fiberless virion

SupramoleculeName: phi29 fiberless virion / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Bacillus phage phi29

SupramoleculeName: Bacillus phage phi29 / type: virus / ID: 1 / NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Bacillus subtilis (bacteria) / synonym: BACTERIA(EUBACTERIA)

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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

VitrificationCryogen name: ETHANE / Instrument: REICHERT-JUNG PLUNGER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/ST
DateJun 11, 2008
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 78 / Od range: 1 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 12682

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