[English] 日本語
Yorodumi- PDB-2yt8: Solution structure of the PDZ domain of Amyloid beta A4 precursor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yt8 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the PDZ domain of Amyloid beta A4 precursor protein-binding family A member 3 (Neuron- specific X11L2 protein) (Neuronal Munc18-1-interacting protein 3) (Mint-3) (Adapter protein X11gamma) | ||||||
Components | Amyloid beta A4 precursor protein-binding family A member 3 | ||||||
Keywords | PROTEIN TRANSPORT / structure genomics / PDZ domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of catalytic activity / Neurexins and neuroligins / enzyme inhibitor activity / protein transport / amyloid-beta binding / chemical synaptic transmission / regulation of gene expression / in utero embryonic development / dendritic spine / perinuclear region of cytoplasm ...negative regulation of catalytic activity / Neurexins and neuroligins / enzyme inhibitor activity / protein transport / amyloid-beta binding / chemical synaptic transmission / regulation of gene expression / in utero embryonic development / dendritic spine / perinuclear region of cytoplasm / enzyme binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Dang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Tarada, T. / Seiki, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PDZ domain of Amyloid beta A4 precursor protein-binding family A member 3 (Neuron- specific X11L2 protein) (Neuronal Munc18-1-interacting protein 3) (Mint-3) (Adapter protein X11gamma) Authors: Dang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Tarada, T. / Seiki, M. / Yokoyama, S. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yt8.cif.gz | 543.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yt8.ent.gz | 474.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/2yt8 ftp://data.pdbj.org/pub/pdb/validation_reports/yt/2yt8 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 10000.472 Da / Num. of mol.: 1 / Fragment: UNP residues 483-569, PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: APBA3 / Plasmid: P061128-10 / References: UniProt: O96018 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.0mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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,structures with the lowest energy,target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |