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Yorodumi- EMDB-4161: Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4161 | |||||||||
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Title | Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex | |||||||||
Map data | None | |||||||||
Sample |
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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) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Wild R / Kowal J / Eyring J / Ngwa EM / Aebi M / Locher KP | |||||||||
Funding support | Switzerland, 2 items
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Citation | Journal: Science / Year: 2018 Title: Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation. Authors: Rebekka Wild / Julia Kowal / Jillianne Eyring / Elsy M Ngwa / Markus Aebi / Kaspar P Locher / Abstract: Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to ...Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to glycosylation sites of secretory proteins. Here we describe the atomic structure of yeast OST determined by cryo-electron microscopy, revealing a conserved subunit arrangement. The active site of the catalytic STT3 subunit points away from the center of the complex, allowing unhindered access to substrates. The dolichol-pyrophosphate moiety binds to a lipid-exposed groove of STT3, whereas two noncatalytic subunits and an ordered N-glycan form a membrane-proximal pocket for the oligosaccharide. The acceptor polypeptide site faces an oxidoreductase domain in stand-alone OST complexes or is immediately adjacent to the translocon, suggesting how eukaryotic OSTs efficiently glycosylate a large number of polypeptides before their folding. | |||||||||
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_4161.map.gz | 62.8 MB | EMDB map data format | |
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Header (meta data) | emd-4161-v30.xml emd-4161.xml | 29 KB 29 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4161_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_4161.png | 50.2 KB | ||
Others | emd_4161_additional_1.map.gz emd_4161_additional_2.map.gz | 7.6 MB 96.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4161 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4161 | HTTPS FTP |
-Validation report
Summary document | emd_4161_validation.pdf.gz | 376.9 KB | Display | EMDB validaton report |
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Full document | emd_4161_full_validation.pdf.gz | 376.5 KB | Display | |
Data in XML | emd_4161_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_4161_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4161 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4161 | HTTPS FTP |
-Related structure data
Related structure data | 6eznMC 8agbC 8agcC 8ageC 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_4161.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Map of OST complex in nanodisc, post-processed and masked
File | emd_4161_additional_1.map | ||||||||||||
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Annotation | Map of OST complex in nanodisc, post-processed and masked | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map of OST complex, after nanodisc subtraction, post-processed
File | emd_4161_additional_2.map | ||||||||||||
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Annotation | Map of OST complex, after nanodisc subtraction, post-processed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : yeast oligosaccharyltransferase (OST) complex
+Supramolecule #1: yeast oligosaccharyltransferase (OST) 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 #12: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #13: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #14: 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
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 / Details: 20 mM HEPES, pH 7.5, 150 mM NaCl |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Quantifoil carbon grids (300 mesh, copper) were glow discharged at 25 mA for 40 s. 3.5 ul of nanodisc-reconstituted OST sample at concentration of 0.5 mg/ml was applied onto the grid and ...Details: Quantifoil carbon grids (300 mesh, copper) were glow discharged at 25 mA for 40 s. 3.5 ul of nanodisc-reconstituted OST sample at concentration of 0.5 mg/ml was applied onto the grid and grids were blotted for 3 s and flash-frozen in a mixture of liquid ethane and propane cooled by liquid nitrogen.. |
Details | OST complex reconstituted into nanodisc |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 2 / Number real images: 3915 / Average exposure time: 0.25 sec. / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-6ezn: |