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Structure of ER membrane associated ribosomes in situ
by subtomogram averaging, at 31 A resolution
#1: Surface view with section colored by density value, Surface level: 0.00895, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 0.00895, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 2099 |
|---|---|
| Title | Structure of ER membrane associated ribosomes in situ |
| Map | Reconstruction of ER membrane associated ribosome from canine pancreatic microsomes |
| Sample | ER membrane associated ribosome |
| Keywords |  80S ribosome, translocon, mammalian, ER membrane |
| Authors | Pfeffer S, Brandt F, Hrabe T, Lang S, Eibauer M, Zimmermann R, Foerster F |
| Date | Deposition: 2012-05-14, Header release: 2012-07-25, Map release: 2012-07-25, Last update: 2012-09-26 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.00895, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 0.00895, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  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 | |
| Article | Structure, Vol. 20, Issue 9, Page 1508-18, Year 2012 |
|---|---|
| Title | Structure and 3D arrangement of endoplasmic reticulum membrane-associated ribosomes. |
| Authors | Stefan 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. |
| Keywords | Animals, Cryoelectron Microscopy, Dogs, Electron Microscope Tomography, Endoplasmic Reticulum, Rough (ultrastructure), Intracellular Membranes (ultrastructure), Microsomes (ultrastructure), Models, Molecular, Pancreas (cytology), Ribosomes (ultrastructure) |
| Links | PII: S0969-2126(12)00232-8, DOI: 10.1016/j.str.2012.06.010, PubMed: 22819217 |
 Map | |||||||||||||||||||||||||
| File |  EMD-2099.map ( map file in CCP4 format, 8390 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 599.04 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 4.68 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Reconstruction of ER membrane associated ribosome from canine pancreatic microsomes | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | ER membrane associated ribosome |
|---|---|
| Number of Components | 1 |
| Oligomeric State | ER membrane associated ribosome |
| Theoretical Mass | 4.5MDa |
| Details | The sample is embedded into its native membrane |
| Component #1: ribosome-eukaryote - Membrane-bound 80S ribosome | |
| Scientific name | Membrane-bound 80S ribosome |
| Theoretical Mass | 4.5 MDa |
| Scientific Name of Species | Canis lupus familiaris
|
| Common Name of Species | Dog |
| NCBI taxonomy | 9615 |
| Eukaryote | ALL |
| Recombinant expression | No |
| Natural Source | Cell Location: Endoplasmic reticulum Organelle: Endoplasmic reticulum Organ Or Tissue: Pancreas |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 1 mg/ml |
|---|---|
| Specimen Support Details | lacy carbon |
| Specimen State | particle |
| Buffer | Details: 5 mM MgCl2, 140 mM KCl, 10 mM Hepes pH 7.4, 1 mM DTT, protease inhibitor pH: 7.4 |
| Vitrification | |
| Method | Blot for 3 seconds before plunging |
| Cryogen Name | ETHANE |
| Instrument | FEI VITROBOT MARK IV |
| Imaging | |
| Microscope | FEI POLARA 300 |
| Date | 01-JAN-2011 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 50 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 4000 nm - 4000 nm |
| Energy Filter | Energy Filter: Gatan GIF 2002 , Energy Window: 0-10 eV |
| Specimen Holder | |
| Model | OTHER |
| Tilt Angle | -60 degrees - 60 degrees |
| Temperature | 85 K ( 80 - 90 K) |
| Camera | |
| Image Acquisition | |
| Number of Digital Images | 328 |
| Quant Bit Number | 12 |
 Processing | |
| Method | subtomogram averaging |
|---|---|
| 3D reconstruction | |
| Algorithm | Subtomogram averaging |
| Software | PyTom |
| CTF Correction | each particle |
| Resolution By Author | 31 A |
| Resolution Method | FSC at 0.5 cut-off |
| 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. |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-2099.xml (7.3 KB) | ||
|---|---|---|---|
| Map data | emd_2099.map.gz (7.4 MB) | ||
| Images | EMD-2099-pic.tif (145.7 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2099 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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