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Yorodumi- PDB-2dm7: Solution structure of the 14th Ig-like domain of human KIAA1556 p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dm7 | ||||||
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Title | Solution structure of the 14th Ig-like domain of human KIAA1556 protein | ||||||
Components | KIAA1556 protein | ||||||
Keywords | CONTRACTILE PROTEIN / beta-sandwich / ig-fold / Obscurin / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information protein localization to M-band / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / M band / phosphatidylinositol-4-phosphate binding / regulation of small GTPase mediated signal transduction / structural constituent of muscle / sarcomere organization / ankyrin binding ...protein localization to M-band / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / M band / phosphatidylinositol-4-phosphate binding / regulation of small GTPase mediated signal transduction / structural constituent of muscle / sarcomere organization / ankyrin binding / myofibril / NRAGE signals death through JNK / RHOQ GTPase cycle / phosphatidylinositol-3,4,5-trisphosphate binding / RHOA GTPase cycle / titin binding / phosphatidylinositol-4,5-bisphosphate binding / guanyl-nucleotide exchange factor activity / sarcolemma / Z disc / G alpha (12/13) signalling events / nuclear body / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Nagashima, K. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the 14th Ig-like domain of human KIAA1556 protein Authors: Nagashima, K. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dm7.cif.gz | 609.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dm7.ent.gz | 512.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dm7 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dm7 | 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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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11369.551 Da / Num. of mol.: 1 / Fragment: ig-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: KIAA1556 / Plasmid: P051017-23 / Production host: Cell free synthesis / References: UniProt: Q8NHN3, UniProt: Q5VST9*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: 1.17mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 10% D2O, 90% H2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: JEOL ECA / Manufacturer: JEOL / Model: ECA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |