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- EMDB-2099: Structure of ER membrane associated ribosomes in situ -

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Basic information

Database: EMDB / ID: 2099
TitleStructure of ER membrane associated ribosomes in situ
Keywords80S ribosome / translocon / mammalian / ER membrane
SampleER membrane associated ribosome
SourceCanis lupus familiaris / mammal / Dog /
Map dataReconstruction of ER membrane associated ribosome from canine pancreatic microsomes
Methodsubtomogram averaging, at 31 Å resolution
AuthorsPfeffer S / Brandt F / Hrabe T / Lang S / Eibauer M / Zimmermann R / Foerster F
CitationStructure, 2012, 20, 1508-1518

Structure, 2012, 20, 1508-1518 Yorodumi Papers
Structure and 3D arrangement of endoplasmic reticulum membrane-associated ribosomes.
Stefan Pfeffer / Florian Brandt / Thomas Hrabe / Sven Lang / Matthias Eibauer / Richard Zimmermann / Friedrich Förster

DateDeposition: May 14, 2012 / Header (metadata) release: Jul 25, 2012 / Map release: Jul 25, 2012 / Last update: Sep 26, 2012

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.00895
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.00895
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_2099.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
4.68 Å/pix.
= 599.04 Å
128 pix
4.68 Å/pix.
= 599.04 Å
128 pix
4.68 Å/pix.
= 599.04 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.68 Å
Contour Level:0.00895 (by author), 0.00895 (movie #1):
Minimum - Maximum-0.05852651 - 0.08826262
Average (Standard dev.)0.00050413 (0.007813)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 599.04 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.684.684.68
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z599.040599.040599.040
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0590.0880.001

Supplemental data

Sample components

Entire ER membrane associated ribosome

EntireName: ER membrane associated ribosome / Details: The sample is embedded into its native membrane / Number of components: 1 / Oligomeric State: ER membrane associated ribosome
MassTheoretical: 4.5 MDa

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

Ribosome-eukaryoteName: Membrane-bound 80S ribosome / Eukaryote: ALL / Recombinant expression: No
MassTheoretical: 4.5 MDa
SourceSpecies: Canis lupus familiaris / mammal / Dog /
Source (natural)Organelle: Endoplasmic reticulum / Location in cell: Endoplasmic reticulum / Organ or tissue: Pancreas

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 5 mM MgCl2, 140 mM KCl, 10 mM Hepes pH 7.4, 1 mM DTT, protease inhibitor
pH: 7.4
Support filmlacy carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Method: Blot for 3 seconds before plunging

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: Jan 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 4000 nm / Energy filter: Gatan GIF 2002 / Energy window: 0-10 eV
Specimen HolderModel: OTHER / Tilt Angle: -60 - 60 deg. / Temperature: 85 K ( 80 - 90 K)

Image acquisition

Image acquisitionNumber of digital images: 328 / Bit depth: 12

Image processing

ProcessingMethod: 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 reconstructionAlgorithm: Subtomogram averaging / Software: PyTom / CTF correction: each particle / Resolution: 31 Å / Resolution method: FSC 0.5

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