+Open data
-Basic information
Entry | Database: PDB / ID: 5ky0 | ||||||
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Title | mouse POFUT1 in complex with mouse Notch1 EGF12(D464G) and GDP | ||||||
Components |
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Keywords | TRANSFERASE / glycosyltransferase | ||||||
Function / homology | Function and homology information Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / osteoblast fate commitment ...Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation / cardiac chamber formation / epithelial cell fate commitment / negative regulation of pro-B cell differentiation / negative regulation of inner ear auditory receptor cell differentiation / mitral valve formation / cell migration involved in endocardial cushion formation / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / atrioventricular node development / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / Notch-HLH transcription pathway / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / endocardial cushion development / regulation of extracellular matrix assembly / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / fucose metabolic process / regulation of Notch signaling pathway / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cardiac muscle hypertrophy / negative regulation of cell adhesion molecule production / interleukin-17-mediated signaling pathway / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / endocardium development / apoptotic process involved in embryonic digit morphogenesis / glial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / neuron fate commitment / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / neuronal stem cell population maintenance / tissue regeneration / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / calcium-ion regulated exocytosis / pulmonary valve morphogenesis / heart trabecula morphogenesis / negative regulation of biomineral tissue development / endoderm development / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å | ||||||
Authors | Li, Z. / Rini, J.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Recognition of EGF-like domains by the Notch-modifying O-fucosyltransferase POFUT1. Authors: Li, Z. / Han, K. / Pak, J.E. / Satkunarajah, M. / Zhou, D. / Rini, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ky0.cif.gz | 252.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ky0.ent.gz | 208.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ky0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/5ky0 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/5ky0 | HTTPS FTP |
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-Related structure data
Related structure data | 5kxhC 5kxqC 5ky2C 5ky3C 5ky4C 5ky5C 5ky7C 5ky8C 5ky9C 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 / Sugars , 3 types, 4 molecules AB
#1: Protein | Mass: 40457.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pofut1 / Production host: Homo sapiens (human) / References: UniProt: Q91ZW2, peptide-O-fucosyltransferase |
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#2: Protein/peptide | Mass: 4375.868 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Notch1, Motch / Production host: Escherichia coli (E. coli) / References: UniProt: Q01705 |
#3: Sugar |
-Non-polymers , 3 types, 482 molecules
#4: Chemical | ChemComp-GDP / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 2000 MME 50mM Tris pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 58604 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.53→1.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2.79 / CC1/2: 0.842 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→47.108 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.56 Å2 / Biso mean: 29.68 Å2 / Biso min: 11.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.53→47.108 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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