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Yorodumi- PDB-2dlu: Solution structure of the second PDZ domain of human InaD-like protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dlu | ||||||
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Title | Solution structure of the second PDZ domain of human InaD-like protein | ||||||
Components | InaD-like protein | ||||||
Keywords | PROTEIN BINDING / PDZ domain / InaD-like protein / Inadl protein / hINADL / Pals1-associated tight junction protein / Protein associated to tight junctions / INADL / PATJ / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information tight junction assembly / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of apical/basal cell polarity / establishment or maintenance of epithelial cell apical/basal polarity / apical junction complex / centriolar satellite / bicellular tight junction / cell junction / apical part of cell ...tight junction assembly / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of apical/basal cell polarity / establishment or maintenance of epithelial cell apical/basal polarity / apical junction complex / centriolar satellite / bicellular tight junction / cell junction / apical part of cell / intracellular signal transduction / apical plasma membrane / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Inoue, K. / Kurosaki, C. / Izumi, K. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: to be published Title: Solution structure of the second PDZ domain of human InaD-like protein Authors: Inoue, K. / Kurosaki, C. / Izumi, K. / 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 | 2dlu.cif.gz | 599.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dlu.ent.gz | 502 KB | Display | PDB format |
PDBx/mmJSON format | 2dlu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dlu_validation.pdf.gz | 342 KB | Display | wwPDB validaton report |
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Full document | 2dlu_full_validation.pdf.gz | 482.2 KB | Display | |
Data in XML | 2dlu_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 2dlu_validation.cif.gz | 55 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/2dlu ftp://data.pdbj.org/pub/pdb/validation_reports/dl/2dlu | 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: 11142.365 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: INADL, PATJ / Plasmid: P050627-16 / Production host: Cell free synthesis / References: UniProt: Q8NI35 |
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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: 1.11mM U-15N, 13C-labeled protein; 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: 120mM / pH: 7 / 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 lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |