[English] 日本語
Yorodumi- PDB-6s7o: Cryo-EM structure of human oligosaccharyltransferase complex OST-A -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s7o | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of human oligosaccharyltransferase complex OST-A | |||||||||
Components |
| |||||||||
Keywords | TRANSFERASE / N-glycosylation / Oligosaccharyltransferase / OSTA | |||||||||
Function / homology | Function and homology information oligosaccharyltransferase complex binding / oligosaccharyltransferase I complex / oligosaccharyltransferase III complex / Asparagine N-linked glycosylation / membrane-bounded organelle / co-translational protein modification / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine ...oligosaccharyltransferase complex binding / oligosaccharyltransferase I complex / oligosaccharyltransferase III complex / Asparagine N-linked glycosylation / membrane-bounded organelle / co-translational protein modification / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / epithelial cell apoptotic process / azurophil granule membrane / protein glycosylation / Advanced glycosylation endproduct receptor signaling / blastocyst development / SRP-dependent cotranslational protein targeting to membrane / post-translational protein modification / rough endoplasmic reticulum / enzyme activator activity / T cell activation / response to endoplasmic reticulum stress / response to cytokine / protein modification process / regulation of protein stability / melanosome / transferase activity / Maturation of spike protein / nuclear body / inflammatory response / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Neutrophil degranulation / negative regulation of apoptotic process / apoptotic process / 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
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6s7o.cif.gz | 418.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6s7o.ent.gz | 337.2 KB | Display | PDB format |
PDBx/mmJSON format | 6s7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s7o_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6s7o_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6s7o_validation.xml.gz | 84 KB | Display | |
Data in CIF | 6s7o_validation.cif.gz | 118.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/6s7o ftp://data.pdbj.org/pub/pdb/validation_reports/s7/6s7o | HTTPS FTP |
-Related structure data
Related structure data | 10110MC 6s7tC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ... , 5 types, 5 molecules ABDEF
#1: Protein | Mass: 80607.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P46977, dolichyl-diphosphooligosaccharide-protein glycotransferase |
---|---|
#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 , 3 types, 3 molecules CGH
#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 |
---|---|
#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: 16844.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OSTC, DC2, HDCMD45P, HSPC307 / Production host: Homo sapiens (human) / References: UniProt: Q9NRP0 |
-Sugars , 3 types, 3 molecules
#9: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 |
---|---|
#10: 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 |
#11: 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 |
-Non-polymers , 4 types, 19 molecules
#12: Chemical | ChemComp-KZB / ( #13: Chemical | ChemComp-EGY / ( #14: Chemical | #15: Chemical | ChemComp-KZE / [( | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||
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 |
---|---|
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: 68 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 6035 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 424817 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156950 / Symmetry type: POINT |