[English] 日本語
Yorodumi- EMDB-3072: Representative tomogram of canine pancreatic rough Endoplasmic Re... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3072 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Representative tomogram of canine pancreatic rough Endoplasmic Reticulum vesicles | |||||||||
Map data | Representative tomogram of canine pancreatic rough Endoplasmic Reticulum vesicles. | |||||||||
Sample |
| |||||||||
Keywords | Ribosome / Sec61 / Translocon / Endoplasmic Reticulum / Cryoelectron Tomography / Subtomogram Analysis | |||||||||
Biological species | Canis lupus familiaris (dog) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Pfeffer S / Burbaum L / Unverdorben P / Pech M / Chen Y / Zimmermann R / Beckmann R / Foerster F | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structure of the native Sec61 protein-conducting channel. Authors: Stefan Pfeffer / Laura Burbaum / Pia Unverdorben / Markus Pech / Yuxiang Chen / Richard Zimmermann / Roland Beckmann / Friedrich Förster / Abstract: In mammalian cells, secretory and membrane proteins are translocated across or inserted into the endoplasmic reticulum (ER) membrane by the universally conserved protein-conducting channel Sec61, ...In mammalian cells, secretory and membrane proteins are translocated across or inserted into the endoplasmic reticulum (ER) membrane by the universally conserved protein-conducting channel Sec61, which has been structurally studied in isolated, detergent-solubilized states. Here we structurally and functionally characterize native, non-solubilized ribosome-Sec61 complexes on rough ER vesicles using cryo-electron tomography and ribosome profiling. Surprisingly, the 9-Å resolution subtomogram average reveals Sec61 in a laterally open conformation, even though the channel is not in the process of inserting membrane proteins into the lipid bilayer. In contrast to recent mechanistic models for polypeptide translocation and insertion, our results indicate that the laterally open conformation of Sec61 is the only conformation present in the ribosome-bound translocon complex, independent of its functional state. Consistent with earlier functional studies, our structure suggests that the ribosome alone, even without a nascent chain, is sufficient for lateral opening of Sec61 in a lipid environment. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3072.map.gz | 96.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3072-v30.xml emd-3072.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | EMD-3072.tif | 398.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3072 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3072 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_3072.map.gz / Format: CCP4 / Size: 101.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Representative tomogram of canine pancreatic rough Endoplasmic Reticulum vesicles. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 20.96 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Representative tomogram of canine pancreatic rough Endoplasmic Re...
Entire | Name: Representative tomogram of canine pancreatic rough Endoplasmic Reticulum vesicles. |
---|---|
Components |
|
-Supramolecule #1000: Representative tomogram of canine pancreatic rough Endoplasmic Re...
Supramolecule | Name: Representative tomogram of canine pancreatic rough Endoplasmic Reticulum vesicles. type: sample / ID: 1000 / Number unique components: 2 |
---|
-Supramolecule #1: Membrane-bound 80S ribosome
Supramolecule | Name: Membrane-bound 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL |
---|---|
Source (natural) | Organism: Canis lupus familiaris (dog) / synonym: Dog / Tissue: Pancreas |
-Macromolecule #1: ER protein translocon
Macromolecule | Name: ER protein translocon / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI |
---|---|
Source (natural) | Organism: Canis lupus familiaris (dog) / synonym: Dog / Tissue: Pancreas / Organelle: Endoplasmic Reticulum |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
---|---|
Buffer | pH: 7.6 / Details: 20mM Hepes, 50mM KCl; 2mM MgCl2 |
Grid | Details: Lacey carbon molybdenum grid |
Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 70 % / Instrument: FEI VITROBOT MARK IV / Method: Blot 3 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm |
Specialist optics | Energy filter - Name: Gatan |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 2 ° |
Date | Jun 18, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Average electron dose: 100 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each tilt image |
---|---|
Final reconstruction | Software - Name: PyTom, tom_toolbox, av3_toolbox / Number images used: 61 |
Details | Tomogram reconstruction was accomplished using PyTom. |