|Entry||Database: EMDB / ID: 3405|
|Title||Mammalian 80S Ribosomes Associate with a Novel Vesicular Organelle|
|Keywords||Ribosome / secretion / vesicle|
|Sample||Ribosome Associated Vesicle membrane-bound 80S ribosome|
|Source||Rattus norvegicus / mammal / Rat / ドブネズミ, どぶねずみ /|
|Map data||Reconstruction of Ribosome Associated Vesicle membrane-bound 80S ribosome|
|Authors||Carter SD / Hampton CM / Langlois R / Grassucci RA / Farino ZJ / Morgenstern TM / Rice WJ / Velasco KR / Wigge C / Xu Y / Koller A / Melero R / Mitchell WG / Yi E / Aguilar JI / Levy ES / Greenberg NL / Li W / Courel M / Mahata SK / Freyberg R / Javitch JA / Di Paolo G / Chen EI / Chan RB / Carazo JM / Area-Gomez E / Jensen GJ / Frank J / Freyberg Z|
|Date||Deposition: Mar 30, 2016 / Header (metadata) release: May 4, 2016 / Map release: Aug 2, 2017 / Last update: Aug 2, 2017|
Downloads & links
|File||emd_3405.map.gz (map file in CCP4 format, 41595 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.62 Å|
CCP4 map header:
-Entire Ribosome Associated Vesicle membrane-bound 80S ribosome
|Entire||Name: Ribosome Associated Vesicle membrane-bound 80S ribosome|
Number of components: 1
-Component #1: ribosome-eukaryote, Membrane-bound 80S ribosome
|Ribosome-eukaryote||Name: Membrane-bound 80S ribosome / a.k.a: 80S ribosome / Eukaryote: ALL / Recombinant expression: No|
|Mass||Theoretical: 3 MDa / Experimental: 3 MDa|
|Source||Species: Rattus norvegicus / mammal / Rat / ドブネズミ, どぶねずみ /|
|Source (natural)||Organelle: Ribosome Associated Vesicles / Location in cell: Cytoplasm / Cell: INS-1E insulinoma cells|
|Support film||200 mesh gold grid with thin carbon support|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 150 K / Humidity: 100 % / Method: Blot for 8 seconds before plunging|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300 / Date: Mar 30, 2014 / Details: Weak beam illumination|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 15500 X (nominal), 18977 X (calibrated)|
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 6000 nm
|Specimen Holder||Model: GATAN HELIUM / Tilt Angle: -60 - 60 deg. / Temperature: 80 K ( 80 - 93 K)|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: subtomogram averaging / Number of subtomograms: 1230 / Applied symmetry: C1 (asymmetric)|
Details: The subtomograms were manually selected using the EMAN2 software package.
|3D reconstruction||Algorithm: Tomography / Euler angles: SPIDER: theta +/- 60 degrees / Software: ETOMO/Serial, EM|
Details: Final maps were calculated from five averaged datasets
Resolution method: FSC 0.143, gold-standard
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