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- EMDB-4317: Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Boun... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4317 | ||||||||||||||||||
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Title | Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Non-programmed 80S Ribosome | ||||||||||||||||||
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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 / 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 / negative regulation of ubiquitin-dependent protein catabolic process / cellular response to actinomycin D / rough endoplasmic reticulum / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-translational protein modification / guanyl-nucleotide exchange factor activity / ribosomal large subunit biogenesis / positive regulation of translation / cellular response to gamma radiation / phospholipid binding / transcription coactivator binding / mRNA 5'-UTR binding / rRNA processing / ribosome biogenesis / ribosome binding / retina development in camera-type eye / regulation of translation / heparin binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / protein stabilization / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / synapse / positive regulation of cell population proliferation / 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 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||||||||||||||
![]() | Braunger K / Becker T / Beckmann R | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 432.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 81.4 KB 81.4 KB | Display Display | ![]() |
Images | ![]() | 75.5 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Others | ![]() | 436.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ftjMC ![]() 4306C ![]() 4307C ![]() 4308C ![]() 4309C ![]() 4310C ![]() 4311C ![]() 4312C ![]() 4313C ![]() 4314C ![]() 4315C ![]() 4316C ![]() 6ftgC ![]() 6ftiC C: citing same article ( M: atomic model generated by this map |
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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
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Voxel size | X=Y=Z: 1.1924 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_4317_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Mammalian Oligosaccharyltransferase in complex with Sec61 and the...
+Supramolecule #1: Mammalian Oligosaccharyltransferase in complex with Sec61 and the...
+Supramolecule #2: 60S Ribosomal Subunit
+Supramolecule #3: Sec61 protein conducting channel
+Supramolecule #4: 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: uL8
+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: Ribosomal protein L22
+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: uL29
+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 rRNA
+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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 28.0 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: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90895 |
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Initial angle assignment | Type: OTHER / Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: OTHER / Software - Name: RELION (ver. 2.1) |