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- EMDB-2050: Capsid structure and its Stability at the Late Stages of Bacterio... -

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Basic information

Entry
Database: EMDB / ID: 2050
TitleCapsid structure and its Stability at the Late Stages of Bacteriophage SPP1 Assembly
KeywordsBacteriophage Capsid SPP1
SampleCapsid of SPP1 lacking the auxiliary protein gp12
SourceBacillus phage SPP1 / virus / image: Bacillus subtilis
Map dataReconstruction of an SPP1 capsid that lacks the auxillary protein gp12
Methodsingle particle (icosahedral) reconstruction, at 15.1 A 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 StrPapers
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 16, 2012 / Map release: Jun 14, 2012 / Last update: Mar 14, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_2050.map.gz (map file in CCP4 format, 524289 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.49 A/pix
= 762.88 A
512 pix
1.49 A/pix
= 762.88 A
512 pix
1.49 A/pix
= 762.88 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.49 A
Density
Contour Level:5 (by author), 5 (movie #1):
Minimum - Maximum-22.61569023 - 28.6905098
Average (Standard dev.)-1E-8 (3.00000048)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin-255-256-256
Limit256255255
Spacing512512512
CellA=B=C: 762.88 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.491.491.49
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z762.880762.880762.880
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-256-255-256
NC/NR/NS512512512
D min/max/mean-22.61628.691-0.000

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Supplemental data

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Sample components

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Entire Capsid of SPP1 lacking the auxiliary protein gp12

EntireName: Capsid of SPP1 lacking the auxiliary protein gp12 / Number of components: 1 / Oligomeric State: Icosahedron

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Component #1: virus, Bacillus phage SPP1

VirusName: Bacillus phage SPP1 / Class: OTHER / Empty: No / 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 /
Host category: BACTERIA(EUBACTERIA)

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Experimental details

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Sample preparation

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

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS / Date: Mar 1, 2010 / Details: low-dose imaging procedure
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GENERIC CCD

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 3200 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Angular reconstitution / Software: Imagic / CTF correction: Phase flipping / Resolution: 15.1 A / Resolution method: FSC 0.5

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