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

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Basic information

Entry
Database: EMDB / ID: EMD-5383
TitleMarine Bacteriophage SIO-2 with T12 symmetry (Procapsid)
Map dataSIO-2 prophage
Sample
  • Sample: Marine Phage SIO-2
  • Virus: Vibrio phage SIO-2 (virus)
Keywordsprocapsid / Marine Bacteriophage / Phage / Virus / Decoration Proteins / Ig-like
Biological speciesVibrio phage SIO-2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
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.
History
DepositionJan 10, 2012-
Header (metadata) releaseJan 12, 2012-
Map releaseJan 12, 2012-
UpdateMar 14, 2012-
Current statusMar 14, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5383.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSIO-2 prophage
Voxel sizeX=Y=Z: 3.9 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-6.16991615 - 13.713181499999999
Average (Standard dev.)0.19893758 (±1.02901757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin101010
Dimensions180180180
Spacing180180180
CellA=B=C: 702.0 Å
α=β=γ: 90.0 °

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
Components
  • Sample: Marine Phage SIO-2
  • Virus: Vibrio phage SIO-2 (virus)

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Supramolecule #1000: Marine Phage SIO-2

SupramoleculeName: Marine Phage SIO-2 / type: sample / ID: 1000 / Details: procapsid / Oligomeric state: immature capsid / Number unique components: 1
Molecular weightTheoretical: 12.2 MDa

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Supramolecule #1: Vibrio phage SIO-2

SupramoleculeName: Vibrio phage SIO-2 / type: virus / ID: 1 / Name.synonym: SIO-2 / Details: particles were present with mature phage prep / NCBI-ID: 700512 / Sci species name: Vibrio phage SIO-2 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: SIO-2
Host (natural)Organism: Vibrio sp. SWAT-3 / synonym: BACTERIA(EUBACTERIA)
Molecular weightTheoretical: 12.2 MDa
Virus shellShell ID: 1 / Name: gene84 / Diameter: 600 Å / T number (triangulation number): 12

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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

BufferDetails: 100 kDa-filtered autoclaved seawater
GridDetails: 200 mesh Cu grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 78 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 80000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 80000
Sample stageSpecimen holder: Gatan CT3500 / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 78 K / Max: 78 K / Average: 78 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 210K times magnification
DetailsCollected using Leginon software
DateJun 13, 2009
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 0.975 µm / Number real images: 6628 / Average electron dose: 30 e/Å2

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Image processing

CTF correctionDetails: whole micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN and Frealign / Number images used: 1179
Detailsparticles automatically selected and manually edited

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