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- EMDB-2052: Capsid structure and its Stability at the Late Stages of Bacterio... -

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Basic information

Database: EMDB / ID: 2052
TitleCapsid structure and its Stability at the Late Stages of Bacteriophage SPP1 Assembly
KeywordsBacteriophage Capsid SPP1
SampleCapsid of SPP1
SourceBacillus phage SPP1 / virus / image: Bacillus subtilis
Map dataReconstruction of an SPP1 capsid after DNA ejection
Methodsingle particle (icosahedral) reconstruction, at 10.5 Å resolution
AuthorsWhite HE / Sherman MB / Brasiles S / Jacquet E / Seavers P / Tavares P / Orlova EV
CitationJ. Virol., 2012, 86, 6768-6777

J. Virol., 2012, 86, 6768-6777 Yorodumi Papers
Capsid structure and its stability at the late stages of bacteriophage SPP1 assembly.
Helen E White / Michael B Sherman / Sandrine Brasilès / Eric Jacquet / Philippa Seavers / Paulo Tavares / Elena V Orlova

DateDeposition: Mar 14, 2012 / Header (metadata) release: Mar 23, 2012 / Map release: Jun 14, 2012 / Last update: Jun 14, 2012

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 8
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_2052.map.gz (map file in CCP4 format, 524289 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.49 Å/pix.
= 894. Å
512 pix
1.49 Å/pix.
= 894. Å
512 pix
1.49 Å/pix.
= 894.6 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Voxel sizeX: 1.491 Å / Y: 1.49 Å / Z: 1.49 Å
Contour Level:10 (by author), 8 (movie #1):
Minimum - Maximum-22.61455727 - 34.57154846
Average (Standard dev.)2E-8 (3.00000048)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 894.60004 Å / B: 894 Å / C: 894 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4911.491.49
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z894.600894.000894.000
start NX/NY/NZ-184-184-183
MAP C/R/S123
start NC/NR/NS-256-255-256
D min/max/mean-22.61534.5720.000

Supplemental data

Sample components

Entire Capsid of SPP1

EntireName: Capsid of SPP1 / Number of components: 1 / Oligomeric State: Icosahedron

Component #1: virus, Bacillus phage SPP1

VirusName: Bacillus phage SPP1 / Class: OTHER / Empty: Yes / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Bacillus phage SPP1 / virus / image: Bacillus subtilis
Source (natural)Host Species: Bacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /

Experimental details

Sample preparation

Specimen stateparticle
Support filmholey carbon film grids
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS / Date: Apr 6, 2005 / Details: Low-dose imaging procedure
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Imaging mode: BRIGHT FIELD
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 94 / Scanner: ZEISS SCAI / Sampling size: 7 microns

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 1200 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Angular reconstitution / Software: Imagic / CTF correction: Phase flipping / Resolution: 10.5 Å / Resolution method: FSC 0.5

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