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- EMDB-1116: Conservation of the capsid structure in tailed dsDNA bacteriophag... -

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Basic information

Entry
Database: EMDB / ID: EMD-1116
TitleConservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29.
Map dataThis map is a cryo-EM 3D reconstruction of a fibered, isometric variant of bacteriophage phi29.
Sample
  • Sample: fibered isometric phi29 particle
  • Virus: Bacillus phage phi29 (virus)
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsMorais MC / Choi KH / Chipman PR / Anderson DL / Rossmann MG
CitationJournal: Mol Cell / Year: 2005
Title: Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29.
Authors: Marc C Morais / Kyung H Choi / Jaya S Koti / Paul R Chipman / Dwight L Anderson / Michael G Rossmann /
Abstract: Bacteriophage phi29 is one of the smallest and simplest known dsDNA phages, making it amenable to structural investigations. The three-dimensional structure of a fiberless, isometric variant has been ...Bacteriophage phi29 is one of the smallest and simplest known dsDNA phages, making it amenable to structural investigations. The three-dimensional structure of a fiberless, isometric variant has been determined to 7.9 A resolution by cryo-electron microscopy (cryo-EM), allowing the identification of alpha helices and beta sheets. Their arrangement indicates that the folds of the phi29 and bacteriophage HK97 capsid proteins are similar except for an additional immunoglobulin-like domain of the phi29 protein. An atomic model that incorporates these two domains fits well into the cryo-EM density of the T = 3, fiberless isometric phi29 particle, and cryo-EM structures of fibered isometric and fiberless prolate prohead phi29 particles at resolutions of 8.7 A and 12.7 A, respectively. Thus, phi29 joins the growing number of phages that utilize the HK97 capsid structure, suggesting that this protein fold may be as prevalent in capsids of dsDNA phages as the jelly roll fold is in eukaryotic viruses.
History
DepositionFeb 18, 2005-
Header (metadata) releaseMar 30, 2005-
Map releaseApr 26, 2005-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1yxn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1116.gif

Downloads & links

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Map

FileDownload / File: emd_1116.map.gz / Format: CCP4 / Size: 337.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map is a cryo-EM 3D reconstruction of a fibered, isometric variant of bacteriophage phi29.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.84 Å/pix.
x 449 pix.
= 826.16 Å		1.84 Å/pix.
x 449 pix.
= 826.16 Å		1.84 Å/pix.
x 449 pix.
= 826.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.84 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.49 / Movie #1: 4
Minimum - Maximum-5.894 - 20.832000000000001
Average (Standard dev.)-0.0532458 (±2.48918)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-224-224-224
Dimensions449449449
Spacing449449449
CellA=B=C: 826.16 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.841.841.84
M x/y/z449449449
origin x/y/z0.0000.0000.000
length x/y/z826.160826.160826.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-224-224-224
NX/NY/NZ449449449
MAP C/R/S213
start NC/NR/NS-224-224-224
NC/NR/NS449449449
D min/max/mean-5.89420.832-0.053

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Supplemental data

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Sample components

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Entire : fibered isometric phi29 particle

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

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Supramolecule #1000: fibered isometric phi29 particle

SupramoleculeName: fibered isometric phi29 particle / type: sample / ID: 1000 / Oligomeric state: T3 icosahedron / Number unique components: 1
Molecular weightTheoretical: 14.2 MDa

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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 weightExperimental: 14.2 MDa
Virus shellShell ID: 1 / Diameter: 425 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

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
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 1.84 µm / Number real images: 29 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 / Tilt angle min: 0 / Tilt angle max: 0

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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: 8.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT P3DR POR / Number images used: 5369

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