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Yorodumi- EMDB-10112: Cryo-EM structure of human oligosaccharyltransferase complex OST-B -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10112 | |||||||||
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Title | Cryo-EM structure of human oligosaccharyltransferase complex OST-B | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information : / oligosaccharyltransferase complex binding / : / neutrophil degranulation / Asparagine N-linked glycosylation / membrane-bounded organelle / magnesium ion transport / oligosaccharyltransferase complex / co-translational protein modification / Miscellaneous transport and binding events ...: / oligosaccharyltransferase complex binding / : / neutrophil degranulation / Asparagine N-linked glycosylation / membrane-bounded organelle / magnesium ion transport / oligosaccharyltransferase complex / co-translational protein modification / Miscellaneous transport and binding events / dolichyl-diphosphooligosaccharide-protein glycotransferase / glycoprotein catabolic process / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / magnesium ion transmembrane transporter activity / protein N-linked glycosylation via asparagine / plasma membrane => GO:0005886 / protein N-linked glycosylation / epithelial cell apoptotic process / azurophil granule membrane / protein glycosylation / blastocyst development / Advanced glycosylation endproduct receptor signaling / SRP-dependent cotranslational protein targeting to membrane / response to unfolded protein / specific granule membrane / rough endoplasmic reticulum / enzyme activator activity / response to endoplasmic reticulum stress / post-translational protein modification / response to cytokine / T cell activation / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / cognition / membrane => GO:0016020 / protein modification process / regulation of protein stability / transmembrane transport / melanosome / protein folding / transferase activity / carbohydrate binding / Maturation of spike protein / carbohydrate metabolic process / nuclear body / viral protein processing / inflammatory response / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / apoptotic process / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Ramirez AS / Kowal J / Locher KP | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Science / Year: 2019 Title: Cryo-electron microscopy structures of human oligosaccharyltransferase complexes OST-A and OST-B. Authors: Ana S Ramírez / Julia Kowal / Kaspar P Locher / Abstract: Oligosaccharyltransferase (OST) catalyzes the transfer of a high-mannose glycan onto secretory proteins in the endoplasmic reticulum. Mammals express two distinct OST complexes that act in a ...Oligosaccharyltransferase (OST) catalyzes the transfer of a high-mannose glycan onto secretory proteins in the endoplasmic reticulum. Mammals express two distinct OST complexes that act in a cotranslational (OST-A) or posttranslocational (OST-B) manner. Here, we present high-resolution cryo-electron microscopy structures of human OST-A and OST-B. Although they have similar overall architectures, structural differences in the catalytic subunits STT3A and STT3B facilitate contacts to distinct OST subunits, DC2 in OST-A and MAGT1 in OST-B. In OST-A, interactions with TMEM258 and STT3A allow ribophorin-I to form a four-helix bundle that can bind to a translating ribosome, whereas the equivalent region is disordered in OST-B. We observed an acceptor peptide and dolichylphosphate bound to STT3B, but only dolichylphosphate in STT3A, suggesting distinct affinities of the two OST complexes for protein substrates. | |||||||||
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_10112.map.gz | 194 MB | EMDB map data format | |
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Header (meta data) | emd-10112-v30.xml emd-10112.xml | 29.6 KB 29.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10112_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_10112.png | 136.6 KB | ||
Others | emd_10112_additional_1.map.gz emd_10112_additional_2.map.gz | 128.4 MB 193 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10112 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10112 | HTTPS FTP |
-Validation report
Summary document | emd_10112_validation.pdf.gz | 303.2 KB | Display | EMDB validaton report |
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Full document | emd_10112_full_validation.pdf.gz | 302.3 KB | Display | |
Data in XML | emd_10112_validation.xml.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10112 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10112 | HTTPS FTP |
-Related structure data
Related structure data | 6s7tMC 6s7oC 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_10112.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Additional map: Local resolution filtered map from RELION
File | emd_10112_additional_1.map | ||||||||||||
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Annotation | Local resolution filtered map from RELION | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_10112_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human oligosaccharyltransferase complex OST-B
+Supramolecule #1: Human oligosaccharyltransferase complex OST-B
+Supramolecule #2: Human oligosaccharyltransferase complex
+Supramolecule #3: Magnesium transporter protein 1
+Macromolecule #1: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #3: Transmembrane protein 258
+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 48...
+Macromolecule #8: Magnesium transporter protein 1
+Macromolecule #9: Malectin
+Macromolecule #10: PEPTIDE
+Macromolecule #14: (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)met...
+Macromolecule #15: (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R}...
+Macromolecule #16: MAGNESIUM ION
+Macromolecule #17: (2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotri...
-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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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 14705 / Average exposure time: 8.0 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | 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 |