|Entry||Database: EMDB / ID: 1275|
|Title||The pore structure of the closed RyR1 channel.|
|Sample||ryanodine receptor 1|
|Source||Oryctolagus cuniculus / mammal / rabbit / アナウサギ /|
|Map data||Z-axis of a 3D reconstruction coincides with the 4-fold axis of the channel complex|
|Method||single particle reconstruction, at 9.6 Å resolution|
|Authors||Ludtke SJ / Serysheva II / Hamilton SL / Chiu W|
|Citation||Structure, 2005, 13, 1203-1211|
|Date||Deposition: Jan 19, 2006 / Header (metadata) release: Oct 16, 2006 / Map release: Oct 16, 2007 / Last update: May 26, 2011|
Downloads & links
|File||emd_1275.map.gz (map file in CCP4 format, 65537 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.81 Å|
CCP4 map header:
-Entire ryanodine receptor 1
|Entire||Name: ryanodine receptor 1|
Details: The sample was purified after solubilization with detergent from skeletal muscle cells
Oligomeric State: homotetramer / Number of components: 1
|Mass||Theoretical: 565 kDa|
-Component #1: protein, Ryanodine receptor type 1
|Protein||Name: Ryanodine receptor type 1 / a.k.a: Skeletal muscle calcium release channel / Oligomeric Details: homotetramer / Details: detergent solubilized membrane protein / Recombinant expression: No / Number of Copies: 4|
|Mass||Experimental: 565 kDa|
|Source||Species: Oryctolagus cuniculus / mammal / rabbit / アナウサギ / |
Strain: White New Zealand
|Source (natural)||Organelle: sarcoplasmic reticulum / Location in cell: sarcoplasmic reticulum membrane / Cell: muscle cell / Organ or tissue: fast twitch skeletal muscle|
|External references||InterPro: InterPro: 000699 / Gene Ontology: GO: 0005219|
|Sample solution||Specimen conc.: 2 mg/ml|
Buffer solution: 20 mM Mops, 300 mM KCl, 1 mM DTT,0.4% CHAPS,5%sucrose,1mM EGTA
|Support film||holey carbon 400 mesh Cu grid|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 101 K / Method: Blot for 3 second before plunging|
Details: Vitrification instrument: Thin carbon film supported by holey carbon film
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2010F|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 60000 X (nominal)|
Astigmatism: objective lens astigmatism was corrected at 400,000X
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1370 - 4550 nm
|Specimen Holder||Holder: side entry / Model: GATAN LIQUID NITROGEN / Temperature: 96 K ( 96 - 97 K)|
|Camera||Detector: GENERIC GATAN (4k x 4k)|
|Image acquisition||Number of digital images: 869 / Sampling size: 1.81 microns / Bit depth: 8|
|Processing||Method: single particle reconstruction / Number of class averages: 2294 / Number of projections: 28036 / Applied symmetry: C4 (4 fold cyclic)|
|3D reconstruction||Algorithm: Iterative projection matching and Direct Fourier inversion|
Software: EMAN / CTF correction: CTF correction of each micrograph / Resolution: 9.6 Å / Resolution method: FSC 0.5
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- 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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External links: The 2017 Nobel Prize in Chemistry - Press Release
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