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Yorodumi- PDB-6s22: Crystal structure of the TgGalNAc-T3 in complex with UDP, mangane... -
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-Basic information
Entry | Database: PDB / ID: 6s22 | ||||||
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Title | Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and FGF23c | ||||||
Components |
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Keywords | TRANSFERASE / GalNAc-Ts / GalNAc-T3 / long-range glycosylation preference / (glyco)peptides / Molecular dynamics / specificity / enzyme kinetics / FGF23 / phosphate homeostasis | ||||||
Function / homology | Function and homology information protein O-linked glycosylation via threonine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / type 1 fibroblast growth factor receptor binding / FGFRL1 modulation of FGFR1 signaling / positive regulation of vitamin D 24-hydroxylase activity / negative regulation of hormone secretion / FGFR1c and Klotho ligand binding and activation / regulation of phosphate transport / intracellular phosphate ion homeostasis ...protein O-linked glycosylation via threonine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / type 1 fibroblast growth factor receptor binding / FGFRL1 modulation of FGFR1 signaling / positive regulation of vitamin D 24-hydroxylase activity / negative regulation of hormone secretion / FGFR1c and Klotho ligand binding and activation / regulation of phosphate transport / intracellular phosphate ion homeostasis / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / vitamin D catabolic process / response to sodium phosphate / negative regulation of bone mineralization / phosphate ion homeostasis / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / cellular response to vitamin D / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / cellular response to leptin stimulus / cellular response to interleukin-6 / cellular response to parathyroid hormone stimulus / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / response to magnesium ion / PI3K Cascade / negative regulation of osteoblast differentiation / fibroblast growth factor receptor signaling pathway / calcium ion homeostasis / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / regulation of cell migration / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / ERK1 and ERK2 cascade / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / Post-translational protein phosphorylation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / animal organ morphogenesis / growth factor activity / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / manganese ion binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / carbohydrate binding / cell differentiation / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / Golgi membrane / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of DNA-templated transcription / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Taeniopygia guttata (zebra finch) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | de las Rivas, M. / Daniel, E.J.P. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. ...de las Rivas, M. / Daniel, E.J.P. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. / Marcelo, F. / Hansen, L. / Lostao, A. / Corzana, F. / Clausen, H. / Gerken, T.A. / Hurtado-Guerrero, R. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3. Authors: de Las Rivas, M. / Paul Daniel, E.J. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. / Marcelo, F. / Hansen, L. / ...Authors: de Las Rivas, M. / Paul Daniel, E.J. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. / Marcelo, F. / Hansen, L. / Maeda, R. / Lostao, A. / Corzana, F. / Clausen, H. / Gerken, T.A. / Hurtado-Guerrero, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s22.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s22.ent.gz | 103 KB | Display | PDB format |
PDBx/mmJSON format | 6s22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/6s22 ftp://data.pdbj.org/pub/pdb/validation_reports/s2/6s22 | HTTPS FTP |
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-Related structure data
Related structure data | 6s24C 5nqaS S: Starting model for refinement 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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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AF
#1: Protein | Mass: 72365.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Taeniopygia guttata (zebra finch) / Gene: GALNT3 / Production host: Komagataella pastoris (fungus) References: UniProt: H0ZAB5, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Protein/peptide | Mass: 1409.597 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Note that this is a monoglycopeptide derived from FGF23: NT*PIPRRHTRSA T* denotes T-O-GalNAc Source: (synth.) Homo sapiens (human) / References: UniProt: Q9GZV9 |
-Sugars , 2 types, 2 molecules
#7: Sugar | ChemComp-NAG / |
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#9: Sugar | ChemComp-NGA / |
-Non-polymers , 6 types, 321 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-UDP / | #6: Chemical | ChemComp-MN / | #8: Chemical | ChemComp-GOL / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Morpheus precipitant mix 4, nitrate phosphate buffer and Morpheus buffer System 1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→51.01 Å / Num. obs: 56142 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.996 / Rpim(I) all: 0.053 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.96→2.07 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8407 / CC1/2: 0.637 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NQA Resolution: 1.96→51.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.589 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.312 Å2
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Refinement step | Cycle: 1 / Resolution: 1.96→51.01 Å
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Refine LS restraints |
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