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- EMDB-3405: Mammalian 80S Ribosomes Associate with a Novel Vesicular Organelle -

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Basic information

Entry
Database: EMDB / ID: EMD-3405
TitleMammalian 80S Ribosomes Associate with a Novel Vesicular Organelle
Map dataReconstruction of Ribosome Associated Vesicle membrane-bound 80S ribosome
Sample
  • Sample: Ribosome Associated Vesicle membrane-bound 80S ribosome
  • Complex: Membrane-bound 80S ribosome
KeywordsRibosome / secretion / vesicle
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM
AuthorsCarter 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
CitationJournal: 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
DepositionMar 30, 2016-
Header (metadata) releaseMay 4, 2016-
Map releaseAug 2, 2017-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3406.tif

Downloads & links

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Map

FileDownload / File: emd_3405.map.gz / Format: CCP4 / Size: 39.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Ribosome Associated Vesicle membrane-bound 80S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.62 Å/pix.
x 220 pix.
= 576.4 Å		2.62 Å/pix.
x 220 pix.
= 576.4 Å		2.62 Å/pix.
x 220 pix.
= 576.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.0 / Movie #1: 12
Minimum - Maximum0.0 - 122.880767820000003
Average (Standard dev.)3.25539947 (±11.725924490000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 576.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z576.400576.400576.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.000122.8813.255

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Supplemental data

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Sample components

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Entire : Ribosome Associated Vesicle membrane-bound 80S ribosome

EntireName: Ribosome Associated Vesicle membrane-bound 80S ribosome
Components
  • Sample: Ribosome Associated Vesicle membrane-bound 80S ribosome
  • Complex: Membrane-bound 80S ribosome

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Supramolecule #1000: Ribosome Associated Vesicle membrane-bound 80S ribosome

SupramoleculeName: 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

SupramoleculeName: Membrane-bound 80S ribosome / type: complex / ID: 1 / Name.synonym: 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Rat / Cell: INS-1E insulinoma cells / Organelle: Ribosome Associated Vesicles / Location in cell: Cytoplasm
Molecular weightExperimental: 3 MDa / Theoretical: 3 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

GridDetails: 200 mesh gold grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 150 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 8 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80 K / Max: 93 K / Average: 80 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DetailsWeak beam illumination
DateMar 30, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen 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

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Image processing

DetailsThe subtomograms were manually selected using the EMAN2 software package.
Final reconstructionApplied 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 assignmentDetails: SPIDER: theta +/- 60 degrees

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