|Entry||Database: EMDB / ID: 5383|
|Title||Marine Bacteriophage SIO-2 with T12 symmetry (Procapsid)|
|Map data||SIO-2 prophage|
|Sample||Marine Phage SIO-2:|
|Keywords||procapsid / Marine Bacteriophage / Phage / Virus / Decoration Proteins / Ig-like|
|Source||Vibrio phage SIO-2 (bacteriophage)|
|Method||single particle reconstruction / cryo EM / 15 Å resolution|
|Authors||Lander GC / Baudoux AC / Azam F / Potter CS / Carragher B / Johnson JE|
|Citation||Journal: 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.
|Date||Deposition: Jan 10, 2012 / Header (metadata) release: Jan 12, 2012 / Map release: Jan 12, 2012 / Last update: Mar 14, 2012|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5383.map.gz (map file in CCP4 format, 22783 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 3.9 Å|
CCP4 map header:
-Entire Marine Phage SIO-2
|Entire||Name: Marine Phage SIO-2 / Details: procapsid / Number of components: 1 / Oligomeric State: immature capsid|
|Mass||Theoretical: 12.2 MDa|
-Component #1: virus, Vibrio phage SIO-2
|Virus||Name: 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|
|Mass||Theoretical: 12.2 MDa|
|Species||Species: Vibrio phage SIO-2 (bacteriophage)|
|Source (natural)||Host Species: Vibrio sp. SWAT-3 / Host category: BACTERIA(EUBACTERIA)|
|Shell #1||Name of element: gene84 / Diameter: 600 Å / T number(triangulation number): 12|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: 100 kDa-filtered autoclaved seawater|
|Support film||200 mesh Cu grid|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 78 K / Humidity: 100 % / Method: blot for 4 seconds before plunging / Details: Vitrification instrument: Vitrobot|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20 / Date: Jun 13, 2009 / Details: Collected using Leginon software|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 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 Holder||Holder: Gatan CT3500 / Model: GATAN LIQUID NITROGEN / Temperature: 78 K ( 78 - 78 K)|
|Camera||Detector: TVIPS TEMCAM-F415 (4k x 4k)|
|Image acquisition||Number of digital images: 6628 / Sampling size: 0.975 microns|
|Processing||Method: single particle reconstruction|
Details: particles automatically selected and manually edited
Number of projections: 1179 / Applied symmetry: I (icosahedral)
|3D reconstruction||Algorithm: Projection matching / Software: EMAN, Frealign / CTF correction: whole micrograph / Resolution: 15 Å / Resolution method: FSC 0.5|
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