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- EMDB-1260: Structural changes of bacteriophage phi29 upon DNA packaging and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1260
TitleStructural changes of bacteriophage phi29 upon DNA packaging and release.
Map dataBacteriophage phi29 emptied head. Five fold symmetry was used in the reconstruction
Sample
  • Sample: emptied bacteriophage phi29
  • Virus: Bacillus phage phi29 (virus)
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsXiang Y / Morais MC / Battisti AJ / Grimes S / Jardine PJ / Anderson DL / Rossmann MG
CitationJournal: EMBO J / Year: 2006
Title: Structural changes of bacteriophage phi29 upon DNA packaging and release.
Authors: Ye Xiang / Marc C Morais / Anthony J Battisti / Shelley Grimes / Paul J Jardine / Dwight L Anderson / Michael G Rossmann /
Abstract: Cryo-electron microscopy three-dimensional reconstructions have been made of mature and of emptied bacteriophage phi29 particles without making symmetry assumptions. Comparisons of these structures ...Cryo-electron microscopy three-dimensional reconstructions have been made of mature and of emptied bacteriophage phi29 particles without making symmetry assumptions. Comparisons of these structures with each other and with the phi29 prohead indicate how conformational changes might initiate successive steps of assembly and infection. The 12 adsorption capable 'appendages' were found to have a structure homologous to the bacteriophage P22 tailspikes. Two of the appendages are extended radially outwards, away from the long axis of the virus, whereas the others are around and parallel to the phage axis. The appendage orientations are correlated with the symmetry-mismatched positions of the five-fold related head fibers, suggesting a mechanism for partial cell wall digestion upon rotation of the head about the tail when initiating infection. The narrow end of the head-tail connector is expanded in the mature virus. Gene product 3, bound to the 5' ends of the genome, appears to be positioned within the expanded connector, which may potentiate the release of DNA-packaging machine components, creating a binding site for attachment of the tail.
History
DepositionAug 16, 2006-
Header (metadata) releaseAug 22, 2006-
Map releaseNov 9, 2006-
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: 1.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1260.gif

Downloads & links

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Map

FileDownload / File: emd_1260.map.gz / Format: CCP4 / Size: 23.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage phi29 emptied head. Five fold symmetry was used in the reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.24 Å/pix.
x 184 pix.
= 780.16 Å		4.24 Å/pix.
x 184 pix.
= 780.16 Å		4.24 Å/pix.
x 184 pix.
= 780.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.24 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.57 / Movie #1: 1.4
Minimum - Maximum-7.88175 - 7.53417
Average (Standard dev.)0.00000000139366 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-92-92-92
Dimensions184184184
Spacing184184184
CellA=B=C: 780.16 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.244.244.24
M x/y/z184184184
origin x/y/z0.0000.0000.000
length x/y/z780.160780.160780.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-60
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS-92-92-92
NC/NR/NS184184184
D min/max/mean-7.8827.5340.000

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Supplemental data

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Sample components

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Entire : emptied bacteriophage phi29

EntireName: emptied bacteriophage phi29
Components
  • Sample: emptied bacteriophage phi29
  • Virus: Bacillus phage phi29 (virus)

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Supramolecule #1000: emptied bacteriophage phi29

SupramoleculeName: emptied bacteriophage phi29 / 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 / Details: empty phi29 / NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Bacillus subtilis (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: prolate icosahedron / Diameter: 530 Å / T number (triangulation number): 3

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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

Concentration1 mg/mL
BufferpH: 7.5 / Details: 20mM NaCl, 10mM Tris-HCL,1mM MgCl2
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
DateDec 12, 2008
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 65
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: 12 / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Phase flip
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: 6193

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Atomic model buiding 1

Initial modelPDB ID:

1tub


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: EMFIT
RefinementSpace: REAL

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