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Yorodumi- EMDB-4315: Subtomogram average of OST-containing ribosome-translocon complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4315 | ||||||||||||
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Title | Subtomogram average of OST-containing ribosome-translocon complexes from canine rough microsomal membranes | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information : / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / oligosaccharyltransferase complex / endoplasmic reticulum Sec complex / pronephric nephron development / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / cotranslational protein targeting to membrane / protein N-linked glycosylation via asparagine ...: / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / oligosaccharyltransferase complex / endoplasmic reticulum Sec complex / pronephric nephron development / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / cotranslational protein targeting to membrane / protein N-linked glycosylation via asparagine / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / post-translational 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 / negative regulation of ubiquitin-dependent protein catabolic process / rough endoplasmic reticulum / maturation of LSU-rRNA / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / post-translational protein modification / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / guanyl-nucleotide exchange factor activity / positive regulation of translation / cellular response to gamma radiation / phospholipid binding / mRNA 5'-UTR binding / transcription coactivator binding / rRNA processing / ribosome biogenesis / ribosome binding / regulation of translation / retina development in camera-type eye / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / protein stabilization / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / positive regulation of cell population proliferation / synapse / endoplasmic reticulum membrane / positive regulation of gene expression / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Canis lupus familiaris (dog) / Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) / Dog (dog) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.1 Å | ||||||||||||
Authors | Pfeffer S / Foerster F | ||||||||||||
Funding support | Germany, 3 items
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Citation | Journal: Science / Year: 2018 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4315.map.gz | 13.1 MB | EMDB map data format | |
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Header (meta data) | emd-4315-v30.xml emd-4315.xml | 81.1 KB 81.1 KB | Display Display | EMDB header |
Images | emd_4315.png | 97.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4315 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4315 | HTTPS FTP |
-Validation report
Summary document | emd_4315_validation.pdf.gz | 231.5 KB | Display | EMDB validaton report |
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Full document | emd_4315_full_validation.pdf.gz | 230.6 KB | Display | |
Data in XML | emd_4315_validation.xml.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4315 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4315 | HTTPS FTP |
-Related structure data
Related structure data | 6ftgMC 4306C 4307C 4308C 4309C 4310C 4311C 4312C 4313C 4314C 4316C 4317C 6ftiC 6ftjC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4315.map.gz / Format: CCP4 / Size: 45.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.62 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : 80S ribosome from WT canine rough microsomal membranes bound to t...
+Supramolecule #1: 80S ribosome from WT canine rough microsomal membranes bound to t...
+Supramolecule #2: Sec61 protein conducting channel
+Supramolecule #3: 60S ribosomal subunit
+Supramolecule #4: Mammalian Oligosaccharyltransferase
+Macromolecule #1: uL2
+Macromolecule #2: uL3
+Macromolecule #3: Ribosomal protein L4
+Macromolecule #4: 60S ribosomal protein L5
+Macromolecule #5: 60S ribosomal protein L6
+Macromolecule #6: uL30
+Macromolecule #7: eL8
+Macromolecule #8: uL6
+Macromolecule #9: Ribosomal protein L10 (Predicted)
+Macromolecule #10: Ribosomal protein L11
+Macromolecule #11: eL13
+Macromolecule #12: Ribosomal protein L14
+Macromolecule #13: Ribosomal protein L15
+Macromolecule #14: uL13
+Macromolecule #15: uL22
+Macromolecule #16: uL14
+Macromolecule #17: eL19
+Macromolecule #18: eL20
+Macromolecule #19: eL21
+Macromolecule #20: eL22
+Macromolecule #21: uL14
+Macromolecule #22: Ribosomal protein L24
+Macromolecule #23: uL23
+Macromolecule #24: Ribosomal protein L26
+Macromolecule #25: 60S ribosomal protein L27
+Macromolecule #26: uL15
+Macromolecule #27: 60S ribosomal protein L29
+Macromolecule #28: eL30
+Macromolecule #29: eL31
+Macromolecule #30: eL32
+Macromolecule #31: eL33
+Macromolecule #32: eL34
+Macromolecule #33: eL29
+Macromolecule #34: 60S ribosomal protein L36
+Macromolecule #35: Ribosomal protein L37
+Macromolecule #36: eL38
+Macromolecule #37: eL39
+Macromolecule #38: eL40
+Macromolecule #39: 60s ribosomal protein l41
+Macromolecule #40: eL42
+Macromolecule #41: Ribosomal protein L37a
+Macromolecule #42: eL28
+Macromolecule #43: 60S acidic ribosomal protein P0
+Macromolecule #44: Ribosomal protein L12
+Macromolecule #48: Protein transport protein Sec61 subunit alpha isoform 1
+Macromolecule #49: Protein transport protein Sec61 subunit gamma
+Macromolecule #50: Protein transport protein Sec61 subunit beta
+Macromolecule #51: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #52: TMEM258
+Macromolecule #53: Oligosaccharyltransferase complex subunit OSTC
+Macromolecule #54: OST4
+Macromolecule #55: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #56: DAD1
+Macromolecule #57: OST48
+Macromolecule #58: RPN2
+Macromolecule #45: 28S ribosomal RNA
+Macromolecule #46: 5S ribosomal RNA
+Macromolecule #47: 5.8S ribosomal RNA
+Macromolecule #60: MAGNESIUM ION
+Macromolecule #61: ZINC ION
+Macromolecule #62: [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL |
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Buffer | pH: 7.6 |
Grid | Material: MOLYBDENUM / Support film - Material: CARBON / Support film - topology: LACEY |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Instrument: FEI VITROBOT MARK IV / Details: Blot 3 seconds before plunging.. |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 17600 |
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Extraction | Number tomograms: 211 / Number images used: 27500 / Method: Template matching / Software: (Name: PyTom, TOM Toolbox, AV3) |
CTF correction | Software - Name: PyTom / Details: On each individual tilt image |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 500 / Target criteria: Cross-correlation coefficient |
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Output model | PDB-6ftg: |