|Entry||Database: EMDB / ID: 1434|
|Title||Nautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.|
|Sample||Nautilus pompilius hemocyanin|
|Source||Nautilus pompilius / invertebrata / オウムガイ, オオムガイ, おおむがい|
|Map data||This is a map of the hemocyanin from the mollusc Nautilus pompilius. Mass correlated threshold: 0.006|
|Method||single particle reconstruction, at 9.1 Å resolution|
|Authors||Gatsogiannis C / Moeller A / Depoix F / Meissner U / Markl J|
|Citation||J. Mol. Biol., 2007, 374, 465-486|
|Date||Deposition: Sep 26, 2007 / Header (metadata) release: Sep 26, 2007 / Map release: Sep 30, 2011 / Last update: Oct 10, 2012|
Downloads & links
|File||emd_1434.map.gz (map file in CCP4 format, 65537 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.85 Å|
CCP4 map header:
-Entire Nautilus pompilius hemocyanin
|Entire||Name: Nautilus pompilius hemocyanin|
Oligomeric State: Nautilus pompilius hemocyanin is a decamer of a 350 kDa subunit. Each subunit is composed by 7 paralogous O2 binding functional units.
Number of components: 1
|Mass||Theoretical: 3.5 MDa|
-Component #1: protein, Nautilus pompilius hemocyanin
|Protein||Name: Nautilus pompilius hemocyanin / a.k.a: Nautilus pompilius hemocyanin / Recombinant expression: No|
|Mass||Experimental: 3.5 MDa|
|Source||Species: Nautilus pompilius / invertebrata / オウムガイ, オオムガイ, おおむがい|
|Source (natural)||Organ or tissue: hemolymph|
|Sample solution||Specimen conc.: 0.4 mg/ml|
Buffer solution: 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2, 150mM NaCl
|Support film||400 mesh copper|
|Staining||cryo-EM, no stain|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 86 K / Method: Single side blotting and rapid plunging|
Details: Vitrification instrument: home made. Vitrification carried out in 100 percent nitrogen atmosphere
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER|
|Lens||Magnification: 49000 X (nominal), 49000 X (calibrated) / Cs: 1.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 3300 nm|
|Specimen Holder||Holder: Gatan single-tilt cryoholder / Model: GATAN LIQUID NITROGEN / Temperature: 86 K|
|Camera||Detector: KODAK SO-163 FILM|
|Processing||Method: single particle reconstruction / Number of class averages: 5200 / Number of projections: 16000|
Details: The particles were selected using the automatic selection program boxer
Applied symmetry: C5 (5 fold cyclic)
|3D reconstruction||Algorithm: Common Lines, projection matching / Software: IMAGIC-5 / CTF correction: CTFFIND3 and TRANSFER, IMAGIC 5 / Resolution: 9.1 Å / Resolution method: FSC 0.5|
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- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
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