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- EMDB-15420: Structure of yeast oligosaccharylransferase complex with lipid-li... -
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Open data
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Basic information
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Title | Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide and non-acceptor peptide bound | |||||||||
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![]() | N-glycosylation OST complex / TRANSFERASE | |||||||||
Function / homology | ![]() oligosaccharyltransferase I complex / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / protein glycosylation / endoplasmic reticulum membrane / structural molecule activity / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Ramirez AS / de Capitani M / Pesciullesi G / Kowal J / Bloch JS / Irobalieva RN / Aebi M / Reymond JL / Locher KP | |||||||||
Funding support | ![]()
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 153.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.7 KB 26.7 KB | Display Display | ![]() |
Images | ![]() | 61.3 KB | ||
Filedesc metadata | ![]() | 8.4 KB | ||
Others | ![]() ![]() | 151.5 MB 151.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8agcMC ![]() 4161C ![]() 6eznC ![]() 8agbC ![]() 8ageC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_15420_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15420_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Yeast OST complex with lipid-linked oligosaccharide and non-accep...
+Supramolecule #1: Yeast OST complex with lipid-linked oligosaccharide and non-accep...
+Macromolecule #1: Dolichyl-diphosphooligosaccharide--protein glycotransferase
+Macromolecule #2: OST4 isoform 1
+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: OST3 isoform 1
+Macromolecule #9: PEPTIDE
+Macromolecule #13: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,1...
+Macromolecule #14: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #15: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #16: MANGANESE (II) ION
+Macromolecule #17: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #18: 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate
-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: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75382 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: ANGULAR RECONSTITUTION |