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Structure of ER membrane associated ribosomes in situ

by subtomogram averaging, at 31 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.00895, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.00895, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2099
TitleStructure of ER membrane associated ribosomes in situ
MapReconstruction of ER membrane associated ribosome from canine pancreatic microsomes
SampleER membrane associated ribosome
Keywords80S ribosome, translocon, mammalian, ER membrane
AuthorsPfeffer S, Brandt F, Hrabe T, Lang S, Eibauer M, Zimmermann R, Foerster F
DateDeposition: 2012-05-14, Header release: 2012-07-25, Map release: 2012-07-25, Last update: 2012-09-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.00895, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.00895, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleStructure, Vol. 20, Issue 9, Page 1508-18, Year 2012
TitleStructure and 3D arrangement of endoplasmic reticulum membrane-associated ribosomes.
AuthorsStefan Pfeffer, Florian Brandt, Thomas Hrabe, Sven Lang, Matthias Eibauer, Richard Zimmermann, Friedrich Förster
Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, D-82152 Martinsried, Germany.
KeywordsAnimals, Cryoelectron Microscopy, Dogs, Electron Microscope Tomography, Endoplasmic Reticulum, Rough (ultrastructure), Intracellular Membranes (ultrastructure), Microsomes (ultrastructure), Models, Molecular, Pancreas (cytology), Ribosomes (ultrastructure)
LinksPII: S0969-2126(12)00232-8, DOI: 10.1016/j.str.2012.06.010, PubMed: 22819217
Map
Fileemd_2099.map.gz ( map file in CCP4 format, 8193 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
4.68 A/pix
= 599.04 A
128 pix
4.68 A/pix
= 599.04 A
128 pix
4.68 A/pix
= 599.04 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.00895 (by author), 0.00895 (movie #1):
Minimum - Maximum: -0.05852651 - 0.08826262
Average (Standard dev.): 0.00050413 (0.007813)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
Unit CellA= B= C: 599.04 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.68 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0590.0880.001
Annotation DetailsReconstruction of ER membrane associated ribosome from canine pancreatic microsomes
Supplement
Images
Images
Sample
NameER membrane associated ribosome
Number of Components1
Oligomeric StateER membrane associated ribosome
Theoretical Mass4.5MDa
DetailsThe sample is embedded into its native membrane
Component #1: ribosome-eukaryote - Membrane-bound 80S ribosome
Scientific nameMembrane-bound 80S ribosome
Theoretical Mass4.5 MDa
Scientific Name of SpeciesCanis lupus familiaris

Common Name of SpeciesDog
NCBI taxonomy9615
EukaryoteALL
Recombinant expressionNo
Natural SourceCell Location: Endoplasmic reticulum
Organelle: Endoplasmic reticulum
Organ Or Tissue: Pancreas
Experiment
Sample Preparation
Specimen Conc1 mg/ml
Specimen Support Detailslacy carbon
Specimen Stateparticle
BufferDetails: 5 mM MgCl2, 140 mM KCl, 10 mM Hepes pH 7.4, 1 mM DTT, protease inhibitor
pH: 7.4
Vitrification
MethodBlot for 3 seconds before plunging
Cryogen NameETHANE
InstrumentFEI VITROBOT MARK IV
Imaging
MicroscopeFEI POLARA 300
Date01-JAN-2011
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose50 e/A**2
Illumination ModeFLOOD BEAM
Lens
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus4000 nm - 4000 nm
Energy FilterEnergy Filter: Gatan GIF 2002 , Energy Window: 0-10 eV
Specimen Holder
ModelOTHER
Tilt Angle-60 degrees - 60 degrees
Temperature85 K ( 80 - 90 K)
Camera
Image Acquisition
Number of Digital Images328
Quant Bit Number12
Processing
Methodsubtomogram averaging
3D reconstruction
AlgorithmSubtomogram averaging
SoftwarePyTom
CTF Correctioneach particle
Resolution By Author31 A
Resolution MethodFSC 0.5
Subtomogram Averaging
DetailsThe 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.
Download
Data from EMDB
Header (meta data in XML format)emd-2099.xml (7.3 KB)
Map dataemd_2099.map.gz (7.4 MB)
ImagesEMD-2099-pic.tif (145.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2099
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 4.3 MB
Session file for UCSF-Chimera, 26.7 KB