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Yorodumi- PDB-2kig: A PH domain within OCRL bridges clathrin mediated membrane traffi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kig | ||||||
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Title | A PH domain within OCRL bridges clathrin mediated membrane trafficking to phosphoinositide metabolism | ||||||
Components | Inositol polyphosphate 5-phosphatase II isoform | ||||||
Keywords | ENDOCYTOSIS / HYDROLASE / OCRL / INPP5B / PH / clathrin | ||||||
Function / homology | Function and homology information Synthesis of IP2, IP, and Ins in the cytosol / : / Synthesis of IP3 and IP4 in the cytosol / : / flagellated sperm motility / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation ...Synthesis of IP2, IP, and Ins in the cytosol / : / Synthesis of IP3 and IP4 in the cytosol / : / flagellated sperm motility / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of protein processing / endoplasmic reticulum-Golgi intermediate compartment / phagocytic vesicle membrane / early endosome membrane / spermatogenesis / in utero embryonic development / membrane => GO:0016020 / signal transduction / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Mao, Y. / Hodsdon, M.E. / De Camilli, P. | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: A PH domain within OCRL bridges clathrin-mediated membrane trafficking to phosphoinositide metabolism. Authors: Mao, Y. / Balkin, D.M. / Zoncu, R. / Erdmann, K.S. / Tomasini, L. / Hu, F. / Jin, M.M. / Hodsdon, M.E. / De Camilli, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kig.cif.gz | 962.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kig.ent.gz | 832.5 KB | Display | PDB format |
PDBx/mmJSON format | 2kig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/2kig ftp://data.pdbj.org/pub/pdb/validation_reports/ki/2kig | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 18005.197 Da / Num. of mol.: 1 / Fragment: UNP residues 1-156 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Inpp5b / Production host: Escherichia coli (E. coli) / References: UniProt: Q91ZF8, UniProt: Q8K337*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 20 mM potassium phosphate-1, potasium phosphate / Solvent system: potasium phosphate |
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Sample | Conc.: 20 mM / Component: potassium phosphate-1 |
Sample conditions | pH: 6.4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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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: 200 / Conformers submitted total number: 20 |