|Entry||Database: EMDB / ID: 2099|
|Title||Structure of ER membrane associated ribosomes in situ|
|Keywords||80S ribosome / translocon / mammalian / ER membrane|
|Sample||ER membrane associated ribosome|
|Source||Canis lupus familiaris / mammal / Dog /|
|Map data||Reconstruction of ER membrane associated ribosome from canine pancreatic microsomes|
|Method||subtomogram averaging, at 31 Å resolution|
|Authors||Pfeffer S / Brandt F / Hrabe T / Lang S / Eibauer M / Zimmermann R / Foerster F|
|Citation||Structure, 2012, 20, 1508-1518|
|Date||Deposition: May 14, 2012 / Header (metadata) release: Jul 25, 2012 / Map release: Jul 25, 2012 / Last update: Sep 26, 2012|
Downloads & links
|File||emd_2099.map.gz (map file in CCP4 format, 8193 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 4.68 Å|
CCP4 map header:
-Entire ER membrane associated ribosome
|Entire||Name: ER membrane associated ribosome / Details: The sample is embedded into its native membrane / Number of components: 1 / Oligomeric State: ER membrane associated ribosome|
|Mass||Theoretical: 4.5 MDa|
-Component #1: ribosome-eukaryote, Membrane-bound 80S ribosome
|Ribosome-eukaryote||Name: Membrane-bound 80S ribosome / Eukaryote: ALL / Recombinant expression: No|
|Mass||Theoretical: 4.5 MDa|
|Source||Species: Canis lupus familiaris / mammal / Dog /|
|Source (natural)||Organelle: Endoplasmic reticulum / Location in cell: Endoplasmic reticulum / Organ or tissue: Pancreas|
|Sample solution||Specimen conc.: 1 mg/ml|
Buffer solution: 5 mM MgCl2, 140 mM KCl, 10 mM Hepes pH 7.4, 1 mM DTT, protease inhibitor
|Support film||lacy carbon|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Method: Blot for 3 seconds before plunging|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300 / Date: Jan 1, 2011|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 4000 nm / Energy filter: Gatan GIF 2002 / Energy window: 0-10 eV|
|Specimen Holder||Model: OTHER / Tilt Angle: -60 - 60 deg. / Temperature: 85 K ( 80 - 90 K)|
|Image acquisition||Number of digital images: 328 / Bit depth: 12|
|Processing||Method: subtomogram averaging|
Details: The particles were selected using PyTom and classified by constrained principal component analysis. Average number of projections used in the 3D reconstructions: 1000. Average number of class averages: 1.
|3D reconstruction||Algorithm: Subtomogram averaging / Software: PyTom / CTF correction: each particle / Resolution: 31 Å / Resolution method: FSC 0.5|
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