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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: 3405
TitleMammalian 80S Ribosomes Associate with a Novel Vesicular Organelle
KeywordsRibosome / secretion / vesicle
SampleRibosome Associated Vesicle membrane-bound 80S ribosome
SourceRattus norvegicus / mammal / Rat / ドブネズミ, どぶねずみ /
Map dataReconstruction of Ribosome Associated Vesicle membrane-bound 80S ribosome
Methodsubtomogram averaging
AuthorsCarter 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
CitationNAT.COMMUN.

NAT.COMMUN.
Mammalian 80S Ribosomes Associate with a Novel Vesicular Organelle
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

DateDeposition: Mar 30, 2016 / Header (metadata) release: May 4, 2016 / Map release: Aug 2, 2017 / Last update: Aug 2, 2017

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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
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Supplemental images

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Map

Fileemd_3405.map.gz (map file in CCP4 format, 41595 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
220 pix
2.62 Å/pix.
= 576.4 Å
220 pix
2.62 Å/pix.
= 576.4 Å
220 pix
2.62 Å/pix.
= 576.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.62 Å
Density
Contour Level:12 (by author), 12 (movie #1):
Minimum - Maximum0E-8 - 122.88076782
Average (Standard dev.)3.25539947 (11.72592449)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions220220220
Origin000
Limit219219219
Spacing220220220
CellA=B=C: 576.39996 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
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
Number of components: 1

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Component #1: ribosome-eukaryote, Membrane-bound 80S ribosome

Ribosome-eukaryoteName: Membrane-bound 80S ribosome / a.k.a: 80S ribosome / Eukaryote: ALL / Recombinant expression: No
MassTheoretical: 3 MDa / Experimental: 3 MDa
SourceSpecies: 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

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Experimental details

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Sample preparation

Specimen statecell
Support film200 mesh gold grid with thin carbon support
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 150 K / Humidity: 100 % / Method: Blot for 8 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: Mar 30, 2014 / Details: Weak beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 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 HolderModel: GATAN HELIUM / Tilt Angle: -60 - 60 deg. / Temperature: 80 K ( 80 - 93 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Number of subtomograms: 1230 / Applied symmetry: C1 (asymmetric)
Details: The subtomograms were manually selected using the EMAN2 software package.
3D reconstructionAlgorithm: 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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