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Yorodumi- PDB-6p2r: Structure of S. cerevisiae protein O-mannosyltransferase Pmt1-Pmt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p2r | ||||||
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Title | Structure of S. cerevisiae protein O-mannosyltransferase Pmt1-Pmt2 complex bound to the sugar donor | ||||||
Components |
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Keywords | TRANSFERASE / complex / glycosylation | ||||||
Function / homology | Function and homology information dolichyl-phosphate-mannose-protein mannosyltransferase Pmt1p-Pmt3p dimer complex / dolichyl-phosphate-mannose-protein mannosyltransferase Pmt5p-Pmt2p dimer complex / dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / dolichyl-phosphate-mannose-protein mannosyltransferase Pmt1p-Pmt2p dimer complex / regulation of endoplasmic reticulum unfolded protein response / fungal-type cell wall biogenesis / protein O-linked mannosylation / protein exit from endoplasmic reticulum / protein O-linked glycosylation ...dolichyl-phosphate-mannose-protein mannosyltransferase Pmt1p-Pmt3p dimer complex / dolichyl-phosphate-mannose-protein mannosyltransferase Pmt5p-Pmt2p dimer complex / dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / dolichyl-phosphate-mannose-protein mannosyltransferase Pmt1p-Pmt2p dimer complex / regulation of endoplasmic reticulum unfolded protein response / fungal-type cell wall biogenesis / protein O-linked mannosylation / protein exit from endoplasmic reticulum / protein O-linked glycosylation / ERAD pathway / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae W303 (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Bai, L. / Li, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structure of the eukaryotic protein O-mannosyltransferase Pmt1-Pmt2 complex. Authors: Lin Bai / Amanda Kovach / Qinglong You / Alanna Kenny / Huilin Li / Abstract: In eukaryotes, a nascent peptide entering the endoplasmic reticulum (ER) is scanned by two Sec61 translocon-associated large membrane machines for protein N-glycosylation and protein O-mannosylation, ...In eukaryotes, a nascent peptide entering the endoplasmic reticulum (ER) is scanned by two Sec61 translocon-associated large membrane machines for protein N-glycosylation and protein O-mannosylation, respectively. While the structure of the eight-protein oligosaccharyltransferase complex has been determined recently, the structures of mannosyltransferases of the PMT family, which are an integral part of ER protein homeostasis, are still unknown. Here we report cryo-EM structures of the Saccharomyces cerevisiae Pmt1-Pmt2 complex bound to a donor and an acceptor peptide at 3.2-Å resolution, showing that each subunit contains 11 transmembrane helices and a lumenal β-trefoil fold termed the MIR domain. The structures reveal the substrate recognition model and confirm an inverting mannosyl-transferring reaction mechanism by the enzyme complex. Furthermore, we found that the transmembrane domains of Pmt1 and Pmt2 share a structural fold with the catalytic subunits of oligosaccharyltransferases, confirming a previously proposed evolutionary relationship between protein O-mannosylation and protein N-glycosylation. | ||||||
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 | 6p2r.cif.gz | 265.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p2r.ent.gz | 213.8 KB | Display | PDB format |
PDBx/mmJSON format | 6p2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p2r_validation.pdf.gz | 970.2 KB | Display | wwPDB validaton report |
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Full document | 6p2r_full_validation.pdf.gz | 996.3 KB | Display | |
Data in XML | 6p2r_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 6p2r_validation.cif.gz | 67.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/6p2r ftp://data.pdbj.org/pub/pdb/validation_reports/p2/6p2r | HTTPS FTP |
-Related structure data
Related structure data | 20240MC 6p25C 6p28C 20237 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
#1: Protein | Mass: 92771.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Gene: PMT1, YDL095W, D2390 / Variant: W303 / Production host: Saccharomyces cerevisiae W303 (yeast) / Variant (production host): W303 References: UniProt: P33775, dolichyl-phosphate-mannose-protein mannosyltransferase | ||||
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#2: Protein | Mass: 86957.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Gene: PMT2, FUN25, YAL023C / Variant: W303 / Production host: Saccharomyces cerevisiae W303 (yeast) / Variant (production host): W303 References: UniProt: P31382, dolichyl-phosphate-mannose-protein mannosyltransferase | ||||
#3: Sugar | #4: Chemical | #5: Chemical | ChemComp-NNM / ( | |
-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 | Name: Protein O-mannosyl transferase complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae W303 (yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae W303 (yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 913730 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 581966 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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