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Yorodumi- EMDB-7336: The Cryo-EM structure of a eukaryotic oligosaccharyl transferase ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7336 | |||||||||
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Title | The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex | |||||||||
Map data | Eukaryotic oligosaccharyl transferase complex | |||||||||
Sample |
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Function / homology | Function and homology information Miscellaneous transport and binding events / oligosaccharyltransferase I complex / dolichol-linked oligosaccharide biosynthetic process / protein O-linked mannosylation / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / glycosyltransferase activity ...Miscellaneous transport and binding events / oligosaccharyltransferase I complex / dolichol-linked oligosaccharide biosynthetic process / protein O-linked mannosylation / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / glycosyltransferase activity / protein glycosylation / protein-disulfide reductase activity / post-translational protein modification / Neutrophil degranulation / nuclear envelope / protein-macromolecule adaptor activity / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Bai L / Li H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2018 Title: The atomic structure of a eukaryotic oligosaccharyltransferase complex. Authors: Lin Bai / Tong Wang / Gongpu Zhao / Amanda Kovach / Huilin Li / Abstract: N-glycosylation is a ubiquitous modification of eukaryotic secretory and membrane-bound proteins; about 90% of glycoproteins are N-glycosylated. The reaction is catalysed by an eight-protein ...N-glycosylation is a ubiquitous modification of eukaryotic secretory and membrane-bound proteins; about 90% of glycoproteins are N-glycosylated. The reaction is catalysed by an eight-protein oligosaccharyltransferase (OST) complex that is embedded in the endoplasmic reticulum membrane. Our understanding of eukaryotic protein N-glycosylation has been limited owing to the lack of high-resolution structures. Here we report a 3.5 Å resolution cryo-electron microscopy structure of the Saccharomyces cerevisiae OST complex, revealing the structures of subunits Ost1-Ost5, Stt3, Wbp1 and Swp1. We found that seven phospholipids mediate many of the inter-subunit interactions, and an Stt3 N-glycan mediates interactions with Wbp1 and Swp1 in the lumen. Ost3 was found to mediate the OST-Sec61 translocon interface, funnelling the acceptor peptide towards the OST catalytic site as the nascent peptide emerges from the translocon. The structure provides insights into co-translational protein N-glycosylation, and may facilitate the development of small-molecule inhibitors that target this process. | |||||||||
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_7336.map.gz | 8.3 MB | EMDB map data format | |
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Header (meta data) | emd-7336-v30.xml emd-7336.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
Images | emd_7336.png | 163.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7336 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7336 | HTTPS FTP |
-Validation report
Summary document | emd_7336_validation.pdf.gz | 356.6 KB | Display | EMDB validaton report |
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Full document | emd_7336_full_validation.pdf.gz | 356.1 KB | Display | |
Data in XML | emd_7336_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_7336_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7336 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7336 | HTTPS FTP |
-Related structure data
Related structure data | 6c26MC M: atomic model generated by this map C: citing same article (ref.) |
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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_7336.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Eukaryotic oligosaccharyl transferase complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.088 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 : oligosaccharyl transferase complex
+Supramolecule #1: oligosaccharyl transferase complex
+Macromolecule #1: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #3: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #4: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #5: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #6: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #7: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #8: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #11: (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)met...
+Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
-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: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 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
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-6c26: |