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Yorodumi- PDB-1wyl: Solution structure of the CH domain of human NEDD9 interacting pr... -
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-Basic information
Entry | Database: PDB / ID: 1wyl | ||||||
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Title | Solution structure of the CH domain of human NEDD9 interacting protein with calponin homology and LIM domains | ||||||
Components | NEDD9 interacting protein with calponin homology and LIM domains | ||||||
Keywords | SIGNALING PROTEIN / CH domain / MICAL / NEDD9 / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / regulation of regulated secretory pathway / NAD(P)H oxidase H2O2-forming activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / actin filament depolymerization / intermediate filament ...hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / regulation of regulated secretory pathway / NAD(P)H oxidase H2O2-forming activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / actin filament depolymerization / intermediate filament / intercellular bridge / actin filament bundle assembly / cytoskeleton organization / FAD binding / negative regulation of protein phosphorylation / actin filament / monooxygenase activity / small GTPase binding / SH3 domain binding / actin filament binding / actin cytoskeleton / actin binding / Factors involved in megakaryocyte development and platelet production / midbody / endosome membrane / negative regulation of apoptotic process / protein kinase binding / signal transduction / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Tomizawa, T. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the CH domain of human NEDD9 interacting protein with calponin homology and LIM domains Authors: Tomizawa, T. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wyl.cif.gz | 638 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wyl.ent.gz | 552.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/1wyl ftp://data.pdbj.org/pub/pdb/validation_reports/wy/1wyl | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11932.241 Da / Num. of mol.: 1 / Fragment: CH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: NICAL / Plasmid: P040315-92 / References: UniProt: Q8TDZ2 |
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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: 1.22mM CH domain U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |