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Yorodumi- EMDB-4316: Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Boun... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4316 | ||||||||||||||||||
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Title | Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Programmed 80S Ribosome | ||||||||||||||||||
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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 | Oryctolagus cuniculus (rabbit) / Canis lupus familiaris (dog) / Rabbit (rabbit) / Dog (dog) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||||||||
Authors | Braunger K / Becker T / Beckmann R | ||||||||||||||||||
Funding support | Germany, 5 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_4316.map.gz | 442.3 MB | EMDB map data format | |
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Header (meta data) | emd-4316-v30.xml emd-4316.xml | 83.1 KB 83.1 KB | Display Display | EMDB header |
Images | emd_4316.png | 76.1 KB | ||
Masks | emd_4316_msk_1.map | 476.8 MB | Mask map | |
Others | emd_4316_additional.map.gz | 445.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4316 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4316 | HTTPS FTP |
-Validation report
Summary document | emd_4316_validation.pdf.gz | 278.9 KB | Display | EMDB validaton report |
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Full document | emd_4316_full_validation.pdf.gz | 278 KB | Display | |
Data in XML | emd_4316_validation.xml.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4316 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4316 | HTTPS FTP |
-Related structure data
Related structure data | 6ftiMC 4306C 4307C 4308C 4309C 4310C 4311C 4312C 4313C 4314C 4315C 4317C 6ftgC 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_4316.map.gz / Format: CCP4 / Size: 476.8 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: 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
File | emd_4316_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_4316_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: 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: 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 #49: Protein transport protein Sec61 subunit alpha isoform 1
+Macromolecule #50: Protein transport protein Sec61 subunit gamma
+Macromolecule #51: Protein transport protein Sec61 subunit beta
+Macromolecule #52: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #53: TMEM258
+Macromolecule #54: Oligosaccharyltransferase complex subunit OSTC
+Macromolecule #55: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #56: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #57: DAD1
+Macromolecule #58: OST48
+Macromolecule #59: RPN1
+Macromolecule #60: Unidentified TM
+Macromolecule #45: p-Site tRNA
+Macromolecule #46: 28S rRNA
+Macromolecule #47: 5S ribosomal RNA
+Macromolecule #48: 5.8S ribosomal RNA
+Macromolecule #62: MAGNESIUM ION
+Macromolecule #63: ZINC ION
+Macromolecule #64: [(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 | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 188900 |
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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) |