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Yorodumi- PDB-7z08: Solution NMR structure of N-acetylglucosaminyltransferase V (GnTV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z08 | ||||||
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Title | Solution NMR structure of N-acetylglucosaminyltransferase V (GnTV) G22L mutant TMD | ||||||
Components | Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A | ||||||
Keywords | MEMBRANE PROTEIN / GnTV / TMD / Golgi / Glycosyltransferase / intramembrane / SPPL3 | ||||||
Function / homology | Function and homology information alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / negative regulation of protein tyrosine phosphatase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein ...alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / negative regulation of protein tyrosine phosphatase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein / viral protein processing / positive regulation of cell migration / Golgi membrane / Golgi apparatus / extracellular exosome / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Silber, M. / Muhle-Goll, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Rep / Year: 2022 Title: Helical stability of the GnTV transmembrane domain impacts on SPPL3 dependent cleavage. Authors: Papadopoulou, A.A. / Stelzer, W. / Silber, M. / Schlosser, C. / Spitz, C. / Haug-Kroper, M. / Straub, T. / Muller, S.A. / Lichtenthaler, S.F. / Muhle-Goll, C. / Langosch, D. / Fluhrer, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z08.cif.gz | 568.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z08.ent.gz | 488.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z08_validation.pdf.gz | 378.1 KB | Display | wwPDB validaton report |
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Full document | 7z08_full_validation.pdf.gz | 556 KB | Display | |
Data in XML | 7z08_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 7z08_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/7z08 ftp://data.pdbj.org/pub/pdb/validation_reports/z0/7z08 | HTTPS FTP |
-Related structure data
Related structure data | 7yyiC 7z07C 7z0bC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3607.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q09328, alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 500 uM GNTV_G22L, trifluoroethanol/water / Details: 80% TFE, 20% H2O / Label: GNTV_G22L / Solvent system: trifluoroethanol/water |
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Sample | Conc.: 500 uM / Component: GNTV_G22L / Isotopic labeling: none |
Sample conditions | Ionic strength: 1 Not defined / Label: GNTV_G22L / pH: 7.0 / Pressure: 1 atm / Temperature: 300 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: cryo probe |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 400 / Conformers submitted total number: 50 |