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Yorodumi- PDB-1x45: Solution structure of the first PDZ domain of amyloid beta A4 pre... -
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-Basic information
Entry | Database: PDB / ID: 1x45 | ||||||
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Title | Solution structure of the first PDZ domain of amyloid beta A4 precursor protein-binding family A, member 1 | ||||||
Components | amyloid beta (A4) precursor protein-binding, family A, member 1 (X11) | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / PDZ domain / Amyloid beta A4 precursor protein-binding family A / member 1 / Neuron-specific XII protein / Adapter protein XII alpha / Neuronal Munc 18-1-interacting protein 1 Mint-1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / glutamate secretion / axo-dendritic transport / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport ...gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / glutamate secretion / axo-dendritic transport / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport / Schaffer collateral - CA1 synapse / multicellular organism growth / synaptic vesicle / nervous system development / amyloid-beta binding / regulation of gene expression / protein-containing complex assembly / chemical synaptic transmission / in utero embryonic development / dendritic spine / cell adhesion / glutamatergic synapse / perinuclear region of cytoplasm / Golgi apparatus / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X.R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: to be published Title: Solution structure of the first PDZ domain of amyloid beta A4 precursor protein-binding family A, member 1 Authors: Qin, X.R. / 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 | 1x45.cif.gz | 549.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x45.ent.gz | 460.4 KB | Display | PDB format |
PDBx/mmJSON format | 1x45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x45_validation.pdf.gz | 340.1 KB | Display | wwPDB validaton report |
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Full document | 1x45_full_validation.pdf.gz | 467 KB | Display | |
Data in XML | 1x45_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 1x45_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/1x45 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/1x45 | 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: 9986.510 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: APBA1, MINT1, X11 / Plasmid: P050118-02 / References: UniProt: Q02410 |
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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: 1.55mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / 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 |