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Yorodumi- PDB-1x5q: Solution structure of the first PDZ domain of scribble homolog pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x5q | ||||||
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Title | Solution structure of the first PDZ domain of scribble homolog protein (hScrib) | ||||||
Components | LAP4 protein | ||||||
Keywords | CELL ADHESION / CELL CYCLE / PDZ domain / LAP4 protein / Scribble homolog protein / hScrib / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation ...extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to adherens junction / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / activation of GTPase activity / establishment or maintenance of epithelial cell apical/basal polarity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / synaptic vesicle endocytosis / immunological synapse / negative regulation of mitotic cell cycle / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / presynapse / cell junction / lamellipodium / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / extracellular exosome / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X.R. / Nagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution structure of the first PDZ domain of scribble homolog protein (hScrib) Authors: Qin, X.R. / Nagashima, T. / 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 | 1x5q.cif.gz | 607.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x5q.ent.gz | 508 KB | Display | PDB format |
PDBx/mmJSON format | 1x5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/1x5q ftp://data.pdbj.org/pub/pdb/validation_reports/x5/1x5q | HTTPS FTP |
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-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: 11241.362 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: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Plasmid: P040628-05 / References: UniProt: Q14160 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: spectrometer_id 1 for 3D_15N_separated_NOESY; spectrometer_id 2 for 3D_13C_separated_NOESY |
-Sample preparation
Details | Contents: 1.20mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 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: 298 K |
-NMR measurement
NMR spectrometer |
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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 |