[English] 日本語
Yorodumi- PDB-6p28: Crystal structure of the MIR domain (aa 337-532) of the S. cerevi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p28 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the MIR domain (aa 337-532) of the S. cerevisiae mannosyltransferase Pmt2 | ||||||
Components | Dolichyl-phosphate-mannose--protein mannosyltransferase 2 | ||||||
Keywords | TRANSFERASE / complex / glycosylation | ||||||
Function / homology | Function and homology information 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 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 / : / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Bai, L. / Li, H. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6p28.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6p28.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 6p28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/6p28 ftp://data.pdbj.org/pub/pdb/validation_reports/p2/6p28 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6p25SC 6p2rC 20237 C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22498.826 Da / Num. of mol.: 1 / Fragment: MIR domain (UNP residues 337-532) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PMT2, FUN25, YAL023C / Production host: Escherichia coli (E. coli) References: UniProt: P31382, dolichyl-phosphate-mannose-protein mannosyltransferase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.06 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG20000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→37.65 Å / Num. obs: 40003 / % possible obs: 96.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.35→1.38 Å / Rmerge(I) obs: 0.023 / Num. unique obs: 17096 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6P25 Resolution: 1.35→37.65 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.924 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.885 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.35→37.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|