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- EMDB-1265: Structural changes of bacteriophage phi29 upon DNA packaging and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1265
TitleStructural changes of bacteriophage phi29 upon DNA packaging and release.
Map dataStructure of bacteriophage phi29 mature head
Sample
  • Sample: phi29 mature particle
  • Virus: Bacillus phage phi29 (virus)
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 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
DepositionSep 12, 2006-
Header (metadata) releaseSep 12, 2006-
Map releaseNov 9, 2006-
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: 2.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1265.gif

Downloads & links

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Map

FileDownload / File: emd_1265.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of bacteriophage phi29 mature head
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.24 Å/pix.
x 200 pix.
= 848. Å		4.24 Å/pix.
x 200 pix.
= 848. Å		4.24 Å/pix.
x 200 pix.
= 848. 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: 1.9 / Movie #1: 2.1
Minimum - Maximum-8.89043 - 11.4315
Average (Standard dev.)0.0104597 (±1.08133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 848 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.244.244.24
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z848.000848.000848.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-8.89011.4320.010

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Supplemental data

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Sample components

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Entire : phi29 mature particle

EntireName: phi29 mature particle
Components
  • Sample: phi29 mature particle
  • Virus: Bacillus phage phi29 (virus)

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Supramolecule #1000: phi29 mature particle

SupramoleculeName: phi29 mature particle / type: sample / ID: 1000
Oligomeric state: capsid protein forms T3 Q5 prolate icosahedron
Number unique components: 1
Molecular weightTheoretical: 33.6 MDa

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Supramolecule #1: Bacillus phage phi29

SupramoleculeName: Bacillus phage phi29 / type: virus / ID: 1 / Name.synonym: M phi29, phi29 mature particle / NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: M phi29, phi29 mature particle
Host (natural)Organism: Bacillus subtilis (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 33.6 MDa
Virus shellShell ID: 1 / Name: capsid-Length-T / Diameter: 530 Å / T number (triangulation number): 3
Virus shellShell ID: 2 / Name: capsid-Width-Q / Diameter: 430 Å / T number (triangulation number): 5

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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: 7.8
Details: 25 mM Tris-HCl pH7.8, 5mM MgCl2, 50mM NaCl and 2mM sodium azide
GridDetails: holey carbon
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 33000
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 68 / Average electron dose: 20 e/Å2 / Details: after scanning, images binned by a factor of 2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: phase flip and amplitude correction for each micrograph
Final two d classificationNumber classes: 20
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 12184

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