+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4257 | |||||||||
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Title | Additional yeast OST cryoEM maps from focused 3D refinements | |||||||||
Map data | Luminal part of OST, Post-processed, masked map, "Map 2" | |||||||||
Sample |
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Biological species | Saccharomyces (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Wild R / Kowal J / Eyring J / Ngwa EM / Aebi M / Locher KP | |||||||||
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_4257.map.gz | 6.6 MB | EMDB map data format | |
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Header (meta data) | emd-4257-v30.xml emd-4257.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4257_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_4257.png | 206.9 KB | ||
Others | emd_4257_additional_1.map.gz emd_4257_additional_2.map.gz emd_4257_additional_3.map.gz | 6 MB 5 MB 4.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4257 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4257 | HTTPS FTP |
-Validation report
Summary document | emd_4257_validation.pdf.gz | 236.7 KB | Display | EMDB validaton report |
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Full document | emd_4257_full_validation.pdf.gz | 235.8 KB | Display | |
Data in XML | emd_4257_validation.xml.gz | 11.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4257 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4257 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4257.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Luminal part of OST, Post-processed, masked map, "Map 2" | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Transmembrane region of OST, Post-processed, masked map, "Map 3"
File | emd_4257_additional_1.map | ||||||||||||
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Annotation | Transmembrane region of OST, Post-processed, masked map, "Map 3" | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: OST1 region of OST, Post-processed, masked map, "Map 5"
File | emd_4257_additional_2.map | ||||||||||||
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Annotation | OST1 region of OST, Post-processed, masked map, "Map 5" | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: SWP1 region of OST, Post-processed, masked map, "Map 4"
File | emd_4257_additional_3.map | ||||||||||||
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Annotation | SWP1 region of OST, Post-processed, masked map, "Map 4" | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : yeast OST
Entire | Name: yeast OST |
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Components |
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-Supramolecule #1: yeast OST
Supramolecule | Name: yeast OST / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces (fungus) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-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: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |