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Yorodumi- PDB-6s7t: Cryo-EM structure of human oligosaccharyltransferase complex OST-B -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s7t | |||||||||
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Title | Cryo-EM structure of human oligosaccharyltransferase complex OST-B | |||||||||
Components |
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Keywords | TRANSFERASE / N-glycosylation / Oligosaccharyltransferase / OSTB | |||||||||
Function / homology | Function and homology information oligosaccharyltransferase complex binding / oligosaccharyltransferase I complex / Asparagine N-linked glycosylation / membrane-bounded organelle / magnesium ion transport / : / neutrophil degranulation / co-translational protein modification / oligosaccharyltransferase complex / glycoprotein catabolic process ...oligosaccharyltransferase complex binding / oligosaccharyltransferase I complex / Asparagine N-linked glycosylation / membrane-bounded organelle / magnesium ion transport / : / neutrophil degranulation / co-translational protein modification / oligosaccharyltransferase complex / glycoprotein catabolic process / Miscellaneous transport and binding events / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / magnesium ion transmembrane transporter activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / epithelial cell apoptotic process / azurophil granule membrane / protein glycosylation / plasma membrane => GO:0005886 / Advanced glycosylation endproduct receptor signaling / blastocyst development / SRP-dependent cotranslational protein targeting to membrane / response to unfolded protein / post-translational protein modification / specific granule membrane / rough endoplasmic reticulum / enzyme activator activity / T cell activation / response to endoplasmic reticulum stress / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / response to cytokine / protein modification process / regulation of protein stability / transmembrane transport / cognition / melanosome / protein folding / transferase activity / carbohydrate binding / Maturation of spike protein / membrane => GO:0016020 / carbohydrate metabolic process / viral protein processing / nuclear body / inflammatory response / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Neutrophil degranulation / negative regulation of apoptotic process / apoptotic process / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Ramirez, A.S. / Kowal, J. / Locher, K.P. | |||||||||
Funding support | Switzerland, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6s7t.cif.gz | 436.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s7t.ent.gz | 347.5 KB | Display | PDB format |
PDBx/mmJSON format | 6s7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s7t_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 6s7t_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6s7t_validation.xml.gz | 83.5 KB | Display | |
Data in CIF | 6s7t_validation.cif.gz | 115.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/6s7t ftp://data.pdbj.org/pub/pdb/validation_reports/s7/6s7t | HTTPS FTP |
-Related structure data
Related structure data | 10112MC 6s7oC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ... , 5 types, 5 molecules ABDEF
#1: Protein | Mass: 93781.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q8TCJ2, dolichyl-diphosphooligosaccharide-protein glycotransferase |
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#2: Protein/peptide | Mass: 4196.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C6T2 |
#4: Protein | Mass: 12503.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61803 |
#5: Protein | Mass: 68656.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04843 |
#6: Protein | Mass: 69347.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04844 |
-Protein , 4 types, 4 molecules CGHI
#3: Protein | Mass: 9083.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61165 |
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#7: Protein | Mass: 50754.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A024RAD5, UniProt: P39656*PLUS |
#8: Protein | Mass: 38081.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAGT1, IAG2, PSEC0084, UNQ628/PRO1244 / Production host: Homo sapiens (human) / References: UniProt: Q9H0U3 |
#9: Protein | Mass: 32270.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14165 |
-Protein/peptide , 1 types, 1 molecules K
#10: Protein/peptide | Mass: 588.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Sugars , 3 types, 4 molecules
#11: Polysaccharide | Source method: isolated from a genetically manipulated source #12: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #13: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 26 molecules
#14: Chemical | ChemComp-EGY / ( #15: Chemical | ChemComp-KZB / ( #16: Chemical | #17: Chemical | ChemComp-0K3 / ( | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 80 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 14705 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1106821 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249725 / Symmetry type: POINT |