|Entry||Database: EMDB / ID: 1900|
|Title||Cryo-EM map of the SPP1 bacteriophage gp19.1-gp21(1-552) complex|
|Keywords||Bacteriophage / SPP1 / Tail tip / gp19.1 / Dit / gp21 / Tal / tail adsorption apparatus / infection mechanism|
|Sample||SPP1 bacteriophage gp19.1-gp21(1-552) complex|
|Source||unidentified phage / virus / Dit, Tal|
|Map data||CCP4 Map file of Bacteriophage spp1 Dit-Tal complex|
|Method||single particle reconstruction, at 26 Å resolution|
|Authors||Goulet A / Lai-Kee-Him J / Veesler D / Auzat I / Robin G / Shepherd DA / Ashcroft AE / Richard E / Lichiere J / Tavares P / Cambillau C / Bron P|
|Citation||J. Biol. Chem., 2011, 286, 25397-25405|
J. Biol. Chem., 2011, 286, 25397-25405 Yorodumi Papers
|Date||Deposition: May 24, 2011 / Header (metadata) release: May 27, 2011 / Map release: Jun 10, 2011 / Last update: Sep 9, 2011|
Downloads & links
|File||emd_1900.map.gz (map file in CCP4 format, 3908 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 4.38 Å|
CCP4 map header:
-Entire SPP1 bacteriophage gp19.1-gp21(1-552) complex
|Entire||Name: SPP1 bacteriophage gp19.1-gp21(1-552) complex / Number of components: 2|
Oligomeric State: This complex assembles two back-to- back stacked gp19.1 ring hexamers, interacting loosely, and two gp21(1-552) trimers interacting with gp19.1 at both ends of the stack
|Mass||Experimental: 730 kDa / Measured by: SEC, MALS, RI, UV, QELS|
-Component #1: protein, gp19.1
|Protein||Name: gp19.1 / a.k.a: Dit / Recombinant expression: Yes|
|Source||Species: unidentified phage / virus / Dit|
-Component #2: protein, gp21(1-552)
|Protein||Name: gp21(1-552) / a.k.a: Tal / Recombinant expression: Yes|
|Source||Species: unidentified phage / virus / Tal|
|Sample solution||Specimen conc.: 0.07 mg/ml / Buffer solution: 10 mM HEPES, 150 mM NaCl / pH: 7.5|
|Support film||Quantifoil R 2/2 grids|
|Vitrification||Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 102.15 K / Humidity: 90 % / Method: Blot for 2s, both sides / Details: Vitrification instrument: Cryoplunge CP3 gatan|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2200FS / Details: Images recorded on a JEOL 2200FS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 45591 X (calibrated)|
Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 2500 nm / Energy filter: Omega JEOL / Energy window: 0-20 eV
|Specimen Holder||Holder: Eucentric / Model: SIDE ENTRY, EUCENTRIC / Temperature: 98.15 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 100 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 10 microns|
|Processing||Method: single particle reconstruction / Number of projections: 15171 / Applied symmetry: D3 (2*3 fold dihedral)|
|3D reconstruction||Algorithm: Projection matching / Software: IMAGIC / CTF correction: Each particle / Resolution: 26 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body / Refinement space: REAL|
Details: The initial fit was done by manual docking followed by refinement using the (fit in map) Chimera plugging
Input PDB model: 2X8K
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