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Yorodumi- EMDB-12808: Cryo-EM structure of yeast Ost6p containing oligosaccharyltransfe... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12808 | |||||||||
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Title | Cryo-EM structure of yeast Ost6p containing oligosaccharyltransferase complex | |||||||||
Map data | Local resolution filtered map from RELION | |||||||||
Sample |
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Function / homology | Function and homology information Miscellaneous transport and binding events / oligosaccharyltransferase I complex / dolichol-linked oligosaccharide biosynthetic process / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / glycosyltransferase activity / protein-disulfide reductase activity ...Miscellaneous transport and binding events / oligosaccharyltransferase I complex / dolichol-linked oligosaccharide biosynthetic process / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / glycosyltransferase activity / protein-disulfide reductase activity / Neutrophil degranulation / post-translational protein modification / nuclear envelope / protein-macromolecule adaptor activity / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Wild R / Neuhaus JD / Eyring J / Irobalieva RN / Kowal J / Lin CW / Locher KP / Aebi M | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Glycobiology / Year: 2021 Title: Functional analysis of Ost3p and Ost6p containing yeast oligosaccharyltransferases. Abstract: The oligosaccharyltransferase (OST) is the central enzyme in the N-glycosylation pathway. It transfers a defined oligosaccharide from a lipid-linker onto the asparagine side chain of proteins. The ...The oligosaccharyltransferase (OST) is the central enzyme in the N-glycosylation pathway. It transfers a defined oligosaccharide from a lipid-linker onto the asparagine side chain of proteins. The yeast OST consists of eight subunits and exists in two catalytically distinct isoforms that differ in one subunit, Ost3p or Ost6p. The cryo-electron microscopy structure of the Ost6p containing complex was found to be highly similar to the Ost3p containing OST. OST enzymes with altered Ost3p/Ost6p subunits were generated and functionally analyzed. The three C-terminal transmembrane helices were responsible for the higher turnover-rate of the Ost3p vs. the Ost6p containing enzyme in vitro and the more severe hypoglycosylation in Ost3p lacking strains in vivo. Glycosylation of specific OST target sites required the N-terminal thioredoxin domain of Ost3p or Ost6p. This Ost3p/Ost6p dependence was glycosylation site but not protein specific. We concluded that the Ost3p/Ost6p subunits modulate the catalytic activity of OST and provide additional specificity for OST substrate recognition. | |||||||||
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_12808.map.gz | 132.8 MB | EMDB map data format | |
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Header (meta data) | emd-12808-v30.xml emd-12808.xml | 26.3 KB 26.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12808_fsc.xml | 17.6 KB | Display | FSC data file |
Images | emd_12808.png | 153.8 KB | ||
Masks | emd_12808_msk_1.map | 216 MB | Mask map | |
Others | emd_12808_additional_1.map.gz emd_12808_additional_2.map.gz | 16.2 MB 156.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12808 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12808 | HTTPS FTP |
-Related structure data
Related structure data | 7ociMC 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_12808.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Local resolution filtered map from RELION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 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_12808_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Postprocessed map from RELION
File | emd_12808_additional_1.map | ||||||||||||
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Annotation | Postprocessed map from RELION | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Gaussian filtered map containing the Ost6p luminal domain
File | emd_12808_additional_2.map | ||||||||||||
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Annotation | Gaussian filtered map containing the Ost6p luminal domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ost6p containing yeast oligosaccharyltransferase complex
+Supramolecule #1: Ost6p containing yeast oligosaccharyltransferase 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 #9: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #12: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #14: Digitonin
+Macromolecule #15: MAGNESIUM ION
+Macromolecule #16: Dolichylphosphate
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE-PROPANE |
Details | This sample was monodisperse |
-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: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 2.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |