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Yorodumi- EMDB-3405: Mammalian 80S Ribosomes Associate with a Novel Vesicular Organelle -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3405 | |||||||||
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Title | Mammalian 80S Ribosomes Associate with a Novel Vesicular Organelle | |||||||||
Map data | Reconstruction of Ribosome Associated Vesicle membrane-bound 80S ribosome | |||||||||
Sample |
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Keywords | Ribosome / secretion / vesicle | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
Authors | Carter SD / Hampton CM / Langlois R / Grassucci RA / Farino ZJ / Morgenstern TM / Rice WJ / Velasco KR / Wigge C / Xu Y ...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 | |||||||||
Citation | Journal: NAT.COMMUN. Title: Mammalian 80S Ribosomes Associate with a Novel Vesicular Organelle 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 / ...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 | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3405.map.gz | 22.5 MB | EMDB map data format | |
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Header (meta data) | emd-3405-v30.xml emd-3405.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | EMD-3406.tif | 664.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3405 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3405 | HTTPS FTP |
-Validation report
Summary document | emd_3405_validation.pdf.gz | 212.2 KB | Display | EMDB validaton report |
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Full document | emd_3405_full_validation.pdf.gz | 211.4 KB | Display | |
Data in XML | emd_3405_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3405 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3405 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3405.map.gz / Format: CCP4 / Size: 39.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Ribosome Associated Vesicle membrane-bound 80S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.62 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Ribosome Associated Vesicle membrane-bound 80S ribosome
Entire | Name: Ribosome Associated Vesicle membrane-bound 80S ribosome |
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Components |
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-Supramolecule #1000: Ribosome Associated Vesicle membrane-bound 80S ribosome
Supramolecule | Name: Ribosome Associated Vesicle membrane-bound 80S ribosome type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Membrane-bound 80S ribosome
Supramolecule | Name: Membrane-bound 80S ribosome / type: complex / ID: 1 / Name.synonym: 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) / synonym: Rat / Cell: INS-1E insulinoma cells / Organelle: Ribosome Associated Vesicles / Location in cell: Cytoplasm |
Molecular weight | Experimental: 3 MDa / Theoretical: 3 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Grid | Details: 200 mesh gold grid with thin carbon support |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 150 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 8 seconds before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 80 K / Max: 93 K / Average: 80 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Details | Weak beam illumination |
Date | Mar 30, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 18977 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 15500 |
Sample stage | Specimen holder model: GATAN HELIUM / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | The subtomograms were manually selected using the EMAN2 software package. |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution method: OTHER / Software - Name: ETOMO/Serial, EM Details: Final maps were calculated from five averaged datasets Number subtomograms used: 1230 |
Final angle assignment | Details: SPIDER: theta +/- 60 degrees |