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Yorodumi- PDB-2eej: Solution Structure of Fourth PDZ domain of PDZ Domain Containing ... -
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-Basic information
Entry | Database: PDB / ID: 2eej | ||||||
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Title | Solution Structure of Fourth PDZ domain of PDZ Domain Containing Protein 1 | ||||||
Components | PDZ domain-containing protein 1 | ||||||
Keywords | METAL BINDING PROTEIN / PDZ domain / regulatory factor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information positive regulation of cation transmembrane transport / carnitine transport / positive regulation of ion transmembrane transporter activity / scavenger receptor binding / xenobiotic detoxification by transmembrane export across the plasma membrane / positive regulation of protein localization to membrane / microvillus membrane / brush border / positive regulation of protein targeting to membrane / protein-membrane adaptor activity ...positive regulation of cation transmembrane transport / carnitine transport / positive regulation of ion transmembrane transporter activity / scavenger receptor binding / xenobiotic detoxification by transmembrane export across the plasma membrane / positive regulation of protein localization to membrane / microvillus membrane / brush border / positive regulation of protein targeting to membrane / protein-membrane adaptor activity / regulation of monoatomic anion transport / protein localization to plasma membrane / PDZ domain binding / brush border membrane / apical plasma membrane / signaling receptor binding / protein-containing complex binding / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Niraula, T.N. / Tomizawa, T. / Koshiba, K. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of Fourth PDZ domain of PDZ Domain Containing Protein 1 Authors: Niraula, T.N. / Tomizawa, T. / Koshiba, K. / Inoue, M. / 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 | 2eej.cif.gz | 536.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eej.ent.gz | 451.3 KB | Display | PDB format |
PDBx/mmJSON format | 2eej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2eej_validation.pdf.gz | 340 KB | Display | wwPDB validaton report |
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Full document | 2eej_full_validation.pdf.gz | 471.9 KB | Display | |
Data in XML | 2eej_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 2eej_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/2eej ftp://data.pdbj.org/pub/pdb/validation_reports/ee/2eej | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
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: 9925.151 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: PDZK1 / Plasmid: P050905-18 / References: UniProt: Q5T2W1 |
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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: 2.65mM PDZ domain U-13C,15N; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D20, 90% H2O 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 / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |