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

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Basic information

Database: EMDB / ID: 5383
TitleMarine Bacteriophage SIO-2 with T12 symmetry (Procapsid)
Map dataSIO-2 prophage
SampleMarine Phage SIO-2:
Keywordsprocapsid / Marine Bacteriophage / Phage / Virus / Decoration Proteins / Ig-like
SourceVibrio phage SIO-2 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / 15 Å resolution
AuthorsLander GC / Baudoux AC / Azam F / Potter CS / Carragher B / Johnson JE
CitationJournal: Structure / Year: 2012
Title: Capsomer dynamics and stabilization in the T = 12 marine bacteriophage SIO-2 and its procapsid studied by CryoEM.
Authors: Gabriel C Lander / Anne-Claire Baudoux / Farooq Azam / Clinton S Potter / Bridget Carragher / John E Johnson
Abstract: We report the subnanometer cryo-electron microscopy (cryoEM) reconstruction of a marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species with significant ecological ...We report the subnanometer cryo-electron microscopy (cryoEM) reconstruction of a marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species with significant ecological importance, including the broadly antagonistic bacterium Vibrio sp. SWAT3. The three-dimensional structure of the 800 Å SIO-2, icosahedrally averaged head of the tailed particle revealed a T = 12 quasi-symmetry not previously described in a bacteriophage. Two morphologically distinct types of auxiliary proteins were also identified; one species bound to the surface of hexamers, and the other bound to pentamers. The secondary structure, evident in the electron density, shows that the major capsid protein has the HK97-like fold. The three-dimensional structure of the procapsid form, also presented here, has no "decoration" proteins and reveals a capsomer organization due to the constraints of the T = 12 symmetry.
DateDeposition: Jan 10, 2012 / Header (metadata) release: Jan 12, 2012 / Map release: Jan 12, 2012 / Last update: Mar 14, 2012

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Structure viewerEM map:
Supplemental images

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

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.9 Å
Contour Level:2.0 (by author), 2 (movie #1):
Minimum - Maximum-6.16991615 - 13.71318150
Average (Standard dev.)0.19893758 (1.02901757)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 702.0 Å
α=β=γ: 90.0 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
start NX/NY/NZ-62-62-62
MAP C/R/S123
start NC/NR/NS101010
D min/max/mean-6.17013.7130.199

Supplemental data

Sample components

Entire Marine Phage SIO-2

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

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 (bacteriophage)
Source (natural)Host Species: Vibrio sp. SWAT-3 / Host category: BACTERIA(EUBACTERIA)
Shell #1Name of element: gene84 / Diameter: 600 Å / T number(triangulation number): 12

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
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

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)

Image acquisition

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

Image processing

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

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