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- EMDB-1281: Determinants of bacteriophage phi29 head morphology. -

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Basic information

Entry
Database: EMDB / ID: EMD-1281
TitleDeterminants of bacteriophage phi29 head morphology.
Map dataThis map is a cryo-EM 3D reconstruction of a fibered, T=4 isometric variant of bacteriophage phi29
Sample
  • Sample: fibered isometric variants of bacteriophage phi29
  • Virus: Bacillus phage phi29 (virus)
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsChoi KH / Morais MC / Anderson DL / Rossmann MG
CitationJournal: Structure / Year: 2006
Title: Determinants of bacteriophage phi29 head morphology.
Authors: Kyung H Choi / Marc C Morais / Dwight L Anderson / Michael G Rossmann /
Abstract: Bacteriophage phi29 requires scaffolding protein to assemble the 450 x 540 A prolate prohead with T = 3 symmetry end caps. In infections with a temperature-sensitive mutant scaffolding protein, ...Bacteriophage phi29 requires scaffolding protein to assemble the 450 x 540 A prolate prohead with T = 3 symmetry end caps. In infections with a temperature-sensitive mutant scaffolding protein, capsids assemble predominantly into 370 A diameter isometric particles with T = 3 symmetry that lack a head-tail connector. However, a few larger, 430 A diameter, particles are also assembled. Cryo-electron microscopy shows that these larger particles are icosahedral with T = 4 symmetry. The prolate prohead, as well as the two isometric capsids with T = 3 and T = 4 symmetry, are composed of similar pentamers and differently skewed hexamers. The skewing of the hexamers in the equatorial region of proheads and in the T = 4 isometric particles reflects their different environments. One of the functions of the scaffolding protein, present in the prohead, may be to stabilize skewed hexamers during assembly.
History
DepositionOct 23, 2006-
Header (metadata) releaseOct 23, 2006-
Map releaseNov 15, 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: 0.54
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.54
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1281.gif

Downloads & links

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Map

FileDownload / File: emd_1281.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map is a cryo-EM 3D reconstruction of a fibered, T=4 isometric variant of bacteriophage phi29
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.68 Å/pix.
x 420 pix.
= 1545.6 Å		3.68 Å/pix.
x 420 pix.
= 1545.6 Å		3.68 Å/pix.
x 420 pix.
= 1545.6 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: 4.66 / Movie #1: 0.54
Minimum - Maximum-5.02178 - 16.562100000000001
Average (Standard dev.)-0.251969 (±2.95932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 1545.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.683.683.68
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z1545.6001545.6001545.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-210-210-210
NC/NR/NS420420420
D min/max/mean-5.02216.562-0.252

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Supplemental data

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Sample components

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Entire : fibered isometric variants of bacteriophage phi29

EntireName: fibered isometric variants of bacteriophage phi29
Components
  • Sample: fibered isometric variants of bacteriophage phi29
  • Virus: Bacillus phage phi29 (virus)

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Supramolecule #1000: fibered isometric variants of bacteriophage phi29

SupramoleculeName: fibered isometric variants of bacteriophage phi29 / type: sample / ID: 1000 / Oligomeric state: T4 icosahderal / Number unique components: 1

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Supramolecule #1: Bacillus phage phi29

SupramoleculeName: Bacillus phage phi29 / type: virus / ID: 1 / Name.synonym: phi29 / NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: phi29
Host (natural)Organism: Bacillus subtilis (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightTheoretical: 17.3 MDa
Virus shellShell ID: 1 / Name: gp8 / Diameter: 430 Å / T number (triangulation number): 4

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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: 7.8 / Details: 25 mM Tris 5 mM MgCl2 50 mM NaCl 2 mM sodium azide
GridDetails: holey carbon
VitrificationCryogen name: ETHANE / Chamber temperature: 113 K

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.903 µm / Nominal defocus min: 1.091 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
DateOct 10, 1997
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 3.68 µm / Number real images: 28 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: CTF correction, phases and amplitudes, for each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN PFT P3DR POR / Number images used: 785

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