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Yorodumi- PDB-2ytw: Solution structure of the PDZ-domain of human protease HTRA 1 pre... -
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-Basic information
Entry | Database: PDB / ID: 2ytw | ||||||
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Title | Solution structure of the PDZ-domain of human protease HTRA 1 precursor | ||||||
Components | Serine protease HTRA1 | ||||||
Keywords | STRUCTURAL PROTEIN / PROTEIN REGULATION / IGF-BINDING PROTEIN CLEAVAGE / PEPTIDASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information chorionic trophoblast cell differentiation / programmed cell death / negative regulation of BMP signaling pathway / growth factor binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Degradation of the extracellular matrix / serine-type peptidase activity / negative regulation of transforming growth factor beta receptor signaling pathway / molecular function activator activity / placenta development ...chorionic trophoblast cell differentiation / programmed cell death / negative regulation of BMP signaling pathway / growth factor binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Degradation of the extracellular matrix / serine-type peptidase activity / negative regulation of transforming growth factor beta receptor signaling pathway / molecular function activator activity / placenta development / collagen-containing extracellular matrix / positive regulation of apoptotic process / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Goroncy, A.K. / Saito, K. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PDZ-domain of human protease HTRA 1 precursor Authors: Goroncy, A.K. / Saito, K. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ytw.cif.gz | 706.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ytw.ent.gz | 596.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ytw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ytw_validation.pdf.gz | 341.9 KB | Display | wwPDB validaton report |
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Full document | 2ytw_full_validation.pdf.gz | 477.3 KB | Display | |
Data in XML | 2ytw_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 2ytw_validation.cif.gz | 56.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/2ytw ftp://data.pdbj.org/pub/pdb/validation_reports/yt/2ytw | HTTPS FTP |
-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: 12774.564 Da / Num. of mol.: 1 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: HTRA1 / Plasmid: P060123-16 References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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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: 1.23mM PDZ DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120 mM / pH: 7 / 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 / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |