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Yorodumi- PDB-6c26: The Cryo-EM structure of a eukaryotic oligosaccharyl transferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c26 | |||||||||
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Title | The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex | |||||||||
Components | (Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ...) x 8 | |||||||||
Keywords | TRANSFERASE / complex / glycosylation | |||||||||
Function / homology | Function and homology information Miscellaneous transport and binding events / oligosaccharyltransferase I complex / 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 ...Miscellaneous transport and binding events / oligosaccharyltransferase I complex / 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 / Neutrophil degranulation / post-translational protein modification / protein-macromolecule adaptor activity / nuclear envelope / protein-containing complex assembly / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Bai, L. / Li, H. | |||||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6c26.cif.gz | 392.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c26.ent.gz | 317.7 KB | Display | PDB format |
PDBx/mmJSON format | 6c26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c26_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6c26_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6c26_validation.xml.gz | 65.4 KB | Display | |
Data in CIF | 6c26_validation.cif.gz | 94.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/6c26 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/6c26 | HTTPS FTP |
-Related structure data
Related structure data | 7336MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ... , 8 types, 8 molecules A15423CB
#1: Protein | Mass: 81604.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P39007, dolichyl-diphosphooligosaccharide-protein glycotransferase |
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#2: Protein | Mass: 54116.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P41543, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#3: Protein | Mass: 9525.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: Q92316, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#4: Protein/peptide | Mass: 3986.696 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: Q99380, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#5: Protein | Mass: 14712.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P46964, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#6: Protein | Mass: 39518.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P48439, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#7: Protein | Mass: 31682.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: Q02795, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#8: Protein | Mass: 49444.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P33767, dolichyl-diphosphooligosaccharide-protein glycotransferase |
-Sugars , 3 types, 3 molecules
#9: Polysaccharide | beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-[beta-D- ...beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#10: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#12: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 8 molecules
#11: Chemical | ChemComp-EGY / ( |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: oligosaccharyl transferase complex / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 823255 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282202 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||
Refine LS restraints |
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