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Yorodumi- PDB-8age: Structure of yeast oligosaccharylransferase complex with acceptor... -
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-Basic information
Entry | Database: PDB / ID: 8age | |||||||||
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Title | Structure of yeast oligosaccharylransferase complex with acceptor peptide bound | |||||||||
Components |
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Keywords | TRANSFERASE / N-glycosylation OST complex | |||||||||
Function / homology | Function and homology information : / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / post-translational protein modification / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Ramirez, A.S. / de Capitani, M. / Pesciullesi, G. / Kowal, J. / Bloch, J.S. / Irobalieva, R.N. / Aebi, M. / Reymond, J.L. / Locher, K.P. | |||||||||
Funding support | Switzerland, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Molecular basis for glycan recognition and reaction priming of eukaryotic oligosaccharyltransferase. Authors: Ana S Ramírez / Mario de Capitani / Giorgio Pesciullesi / Julia Kowal / Joël S Bloch / Rossitza N Irobalieva / Jean-Louis Reymond / Markus Aebi / Kaspar P Locher / Abstract: Oligosaccharyltransferase (OST) is the central enzyme of N-linked protein glycosylation. It catalyzes the transfer of a pre-assembled glycan, GlcNAcManGlc, from a dolichyl-pyrophosphate donor to ...Oligosaccharyltransferase (OST) is the central enzyme of N-linked protein glycosylation. It catalyzes the transfer of a pre-assembled glycan, GlcNAcManGlc, from a dolichyl-pyrophosphate donor to acceptor sites in secretory proteins in the lumen of the endoplasmic reticulum. Precise recognition of the fully assembled glycan by OST is essential for the subsequent quality control steps of glycoprotein biosynthesis. However, the molecular basis of the OST-donor glycan interaction is unknown. Here we present cryo-EM structures of S. cerevisiae OST in distinct functional states. Our findings reveal that the terminal glucoses (Glc) of a chemo-enzymatically generated donor glycan analog bind to a pocket formed by the non-catalytic subunits WBP1 and OST2. We further find that binding either donor or acceptor substrate leads to distinct primed states of OST, where subsequent binding of the other substrate triggers conformational changes required for catalysis. This alternate priming allows OST to efficiently process closely spaced N-glycosylation sites. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8age.cif.gz | 411.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8age.ent.gz | 325.2 KB | Display | PDB format |
PDBx/mmJSON format | 8age.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8age_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8age_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8age_validation.xml.gz | 74.6 KB | Display | |
Data in CIF | 8age_validation.cif.gz | 105.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/8age ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8age | HTTPS FTP |
-Related structure data
Related structure data | 15421MC 4161C 6eznC 8agbC 8agcC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ... , 6 types, 6 molecules ACDEFG
#1: Protein | Mass: 81604.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: STT3, YGL022W / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P39007, dolichyl-diphosphooligosaccharide-protein glycotransferase |
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#3: Protein | Mass: 9525.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: OST5, YGL226C-A, YGL226BC / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q92316 |
#4: Protein | Mass: 14712.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: OST2, GI527_G0005476 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4BUV6 |
#5: Protein | Mass: 54116.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: OST1, GI527_G0003255 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PXA1 |
#6: Protein | Mass: 31340.443 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SWP1, GI527_G0004591 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6V8S2Y6 |
#7: Protein | Mass: 49444.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: WBP1, GI527_G0001785 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H8ULL1 |
-Protein , 2 types, 2 molecules BH
#2: Protein | Mass: 6871.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: OST4, GI527_G0000704 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H8UM72 |
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#8: Protein | Mass: 39518.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: OST3, GI527_G0005459 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3S9 |
-Protein/peptide , 1 types, 1 molecules P
#9: Protein/peptide | Mass: 696.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
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-Sugars , 3 types, 5 molecules
#10: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-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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#11: Polysaccharide | Source method: isolated from a genetically manipulated source #16: Sugar | |
-Non-polymers , 6 types, 24 molecules
#12: Chemical | ChemComp-MN / | ||||||||
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#13: Chemical | ChemComp-CPL / #14: Chemical | ChemComp-PTY / | #15: Chemical | ChemComp-KZB / ( #17: Chemical | ChemComp-323 / | #18: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: Yeast OST complex with acceptor peptide bound / Type: COMPLEX / Entity ID: #2-#5, #7-#8 / Source: NATURAL |
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Molecular weight | Value: 0.284 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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 / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 48.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72993 / Symmetry type: POINT | ||||||||||||||||||||||||
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