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- EMDB-5383: Marine Bacteriophage SIO-2 with T12 symmetry (Procapsid) -

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Basic information

Entry
Database: EMDB / ID: 5383
TitleMarine Bacteriophage SIO-2 with T12 symmetry (Procapsid)
Keywordsprocapsid / Marine Bacteriophage / Phage / Virus / Decoration Proteins / Ig-like
SampleMarine Phage SIO-2
SourceVibrio phage SIO-2 / virus / SIO-2
Map dataSIO-2 prophage
Methodsingle particle (icosahedral) reconstruction, at 15 Å resolution
AuthorsLander GC / Baudoux AC / Azam F / Potter CS / Carragher B / Johnson JE
CitationStructure, 2012, 20, 498-503

Structure, 2012, 20, 498-503 Yorodumi Papers
Capsomer dynamics and stabilization in the T = 12 marine bacteriophage SIO-2 and its procapsid studied by CryoEM.
Gabriel C Lander / Anne-Claire Baudoux / Farooq Azam / Clinton S Potter / Bridget Carragher / John E Johnson

DateDeposition: Jan 10, 2012 / Header (metadata) release: Jan 12, 2012 / Map release: Jan 12, 2012 / Last update: Mar 14, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_5383.map.gz (map file in CCP4 format, 22783 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
3.9 Å/pix.
= 702. Å
180 pix
3.9 Å/pix.
= 702. Å
180 pix
3.9 Å/pix.
= 702. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.9 Å
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-6.16991615 - 13.7131815
Average (Standard dev.)0.19893758 (1.02901757)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin101010
Limit189189189
Spacing180180180
CellA=B=C: 702 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.93.93.9
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z702.000702.000702.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS101010
NC/NR/NS180180180
D min/max/mean-6.17013.7130.199

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Supplemental data

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Sample components

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Entire Marine Phage SIO-2

EntireName: Marine Phage SIO-2 / Details: procapsid / Number of components: 1 / Oligomeric State: immature capsid
MassTheoretical: 12.2 MDa

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Component #1: virus, Vibrio phage SIO-2

VirusName: Vibrio phage SIO-2 / a.k.a: SIO-2 / Class: VIRION / Details: particles were present with mature phage prep / Empty: Yes / Enveloped: No / Isolate: STRAIN
MassTheoretical: 12.2 MDa
SpeciesSpecies: Vibrio phage SIO-2 / virus / SIO-2
Source (natural)Host Species: Vibrio sp. swat-3 / bacteria / Host category: BACTERIA(EUBACTERIA)
Shell #1Name of element: gene84 / Diameter: 600 Å / T number(triangulation number): 12

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 100 kDa-filtered autoclaved seawater
Support film200 mesh Cu grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 78 K / Humidity: 100 % / Method: blot for 4 seconds before plunging / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20 / Date: Jun 13, 2009 / Details: Collected using Leginon software
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal), 80000 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 210K times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1800 - 3000 nm
Specimen HolderHolder: Gatan CT3500 / Model: GATAN LIQUID NITROGEN / Temperature: 78 K ( 78 - 78 K)
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 6628 / Sampling size: 0.975 microns

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction
Details: particles automatically selected and manually edited
Number of projections: 1179 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Projection matching / Software: EMAN and Frealign / CTF correction: whole micrograph / Resolution: 15 Å / Resolution method: FSC 0.5

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