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- EMDB-4308: Subtomogram average of OST-containing ribosome-translocon complex... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4308 | |||||||||
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Title | Subtomogram average of OST-containing ribosome-translocon complexes from STT3B(-/-) HEK cells | |||||||||
![]() | Subtomogram average of OST-containing ribosome-translocon complexes from STT3B(-/-) HEK cells | |||||||||
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Function / homology | ![]() oligosaccharyltransferase III complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / pronephric nephron development / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / cotranslational protein targeting to membrane / Ssh1 translocon complex ...oligosaccharyltransferase III complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / pronephric nephron development / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / protein N-linked glycosylation via asparagine / signal sequence binding / post-translational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane, translocation / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / G1 to G0 transition / protein glycosylation / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein transmembrane transporter activity / cellular response to actinomycin D / rough endoplasmic reticulum / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-translational protein modification / maturation of LSU-rRNA / ribosomal large subunit biogenesis / positive regulation of translation / cellular response to gamma radiation / phospholipid binding / mRNA 5'-UTR binding / transcription coactivator binding / rRNA processing / ribosome biogenesis / ribosome binding / retina development in camera-type eye / regulation of translation / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / protein stabilization / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum membrane / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 30.0 Å | |||||||||
![]() | Pfeffer S / Foerster F | |||||||||
![]() | ![]() Title: Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum. Authors: Katharina Braunger / Stefan Pfeffer / Shiteshu Shrimal / Reid Gilmore / Otto Berninghausen / Elisabet C Mandon / Thomas Becker / Friedrich Förster / Roland Beckmann / ![]() ![]() ![]() Abstract: Protein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and ...Protein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and oligosaccharyltransferase (OST). Here we used different cryo-electron microscopy approaches to determine structures of native and solubilized ribosome-Sec61-OST complexes. A molecular model for the catalytic OST subunit STT3A (staurosporine and temperature sensitive 3A) revealed how it is integrated into the OST and how STT3-paralog specificity for translocon-associated OST is achieved. The OST subunit DC2 was placed at the interface between Sec61 and STT3A, where it acts as a versatile module for recruitment of STT3A-containing OST to the ribosome-Sec61 complex. This detailed structural view on the molecular architecture of the cotranslational machinery for N-glycosylation provides the basis for a mechanistic understanding of glycoprotein biogenesis at the endoplasmic reticulum. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.9 KB 11.9 KB | Display Display | ![]() |
Images | ![]() | 55.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 235.5 KB | Display | ![]() |
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Full document | ![]() | 234.6 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4306C ![]() 4307C ![]() 4309C ![]() 4310C ![]() 4311C ![]() 4312C ![]() 4313C ![]() 4314C ![]() 4315C ![]() 4316C ![]() 4317C ![]() 6ftgC ![]() 6ftiC ![]() 6ftjC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Subtomogram average of OST-containing ribosome-translocon complexes from STT3B(-/-) HEK cells | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : 80S ribosome from STT3B(-/-) HEK cells bound to the endoplasmic r...
Entire | Name: 80S ribosome from STT3B(-/-) HEK cells bound to the endoplasmic reticulum protein translocon |
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Components |
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-Supramolecule #1: 80S ribosome from STT3B(-/-) HEK cells bound to the endoplasmic r...
Supramolecule | Name: 80S ribosome from STT3B(-/-) HEK cells bound to the endoplasmic reticulum protein translocon type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
-Supramolecule #2: OST-containing protein translocon complex of the endoplasmic reticulum
Supramolecule | Name: OST-containing protein translocon complex of the endoplasmic reticulum type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 357 |
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Extraction | Number tomograms: 30 / Number images used: 871 / Software - Name: PyTom |
Final angle assignment | Type: NOT APPLICABLE |