[English] 日本語
Yorodumi- EMDB-4144: Subtomogram average of the ER membrane-associated ribosome from h... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4144 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Subtomogram average of the ER membrane-associated ribosome from human TRAPgamma-deficient fibroblasts | |||||||||
Map data | Subtomogram averages of the ER membrane-associated ribosome from human TRAPgamma-deficient fibroblasts | |||||||||
Sample |
| |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 21.7 Å | |||||||||
Authors | Pfeffer S / Dudek J / Ng BG / Zimmermann R / Freeze HH / Foerster F | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Dissecting the molecular organization of the translocon-associated protein complex. Authors: Stefan Pfeffer / Johanna Dudek / Miroslava Schaffer / Bobby G Ng / Sahradha Albert / Jürgen M Plitzko / Wolfgang Baumeister / Richard Zimmermann / Hudson H Freeze / Benjamin D Engel / Friedrich Förster / Abstract: In eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein ...In eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein (TRAP) complex is an integral component of the translocon, assisting the Sec61 protein-conducting channel by regulating signal sequence and transmembrane helix insertion in a substrate-dependent manner. Here we use cryo-electron tomography (CET) to study the structure of the native translocon in evolutionarily divergent organisms and disease-linked TRAP mutant fibroblasts from human patients. The structural differences detected by subtomogram analysis form a basis for dissecting the molecular organization of the TRAP complex. We assign positions to the four TRAP subunits within the complex, providing insights into their individual functions. The revealed molecular architecture of a central translocon component advances our understanding of membrane protein biogenesis and sheds light on the role of TRAP in human congenital disorders of glycosylation. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4144.map.gz | 37.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4144-v30.xml emd-4144.xml | 8 KB 8 KB | Display Display | EMDB header |
Images | emd_4144.png | 78.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4144 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4144 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4144.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Subtomogram averages of the ER membrane-associated ribosome from human TRAPgamma-deficient fibroblasts | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.62 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : ER membrane-associated ribosome from human TRAPgamma-deficient fi...
Entire | Name: ER membrane-associated ribosome from human TRAPgamma-deficient fibroblasts |
---|---|
Components |
|
-Supramolecule #1: ER membrane-associated ribosome from human TRAPgamma-deficient fi...
Supramolecule | Name: ER membrane-associated ribosome from human TRAPgamma-deficient fibroblasts type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE-PROPANE |
-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 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 21 / Number images used: 973 |
---|---|
Final angle assignment | Type: OTHER |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PyTom / Number subtomograms used: 663 |