+Open data
-Basic information
Entry | Database: PDB / ID: 2css | ||||||
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Title | Solution structure of the PDZ domain of human KIAA0340 protein | ||||||
Components | Regulating synaptic membrane exocytosis protein 1 | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / PDZ domain / Regulating synaptic membrane exocytosis protein 1 / Rab3-interacting molecule 1 / RIM 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 acrosomal vesicle exocytosis / cytoskeleton of presynaptic active zone / small GTPase binding => GO:0031267 / positive regulation of inhibitory postsynaptic potential / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GTPase regulator activity / regulated exocytosis / GABA synthesis, release, reuptake and degradation / calcium ion-regulated exocytosis of neurotransmitter ...acrosomal vesicle exocytosis / cytoskeleton of presynaptic active zone / small GTPase binding => GO:0031267 / positive regulation of inhibitory postsynaptic potential / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GTPase regulator activity / regulated exocytosis / GABA synthesis, release, reuptake and degradation / calcium ion-regulated exocytosis of neurotransmitter / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / regulation of neurotransmitter secretion / presynaptic active zone cytoplasmic component / Glutamate Neurotransmitter Release Cycle / calcium-ion regulated exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / glutamate secretion / response to stimulus / regulation of synaptic vesicle exocytosis / presynaptic active zone / synaptic vesicle exocytosis / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission / visual perception / regulation of membrane potential / secretion / cell projection / intracellular protein transport / regulation of synaptic plasticity / presynaptic membrane / protein-containing complex assembly / transmembrane transporter binding / membrane fusion / synapse / positive regulation of gene expression / RNA binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Inoue, K. / Qin, X.-R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution structure of the PDZ domain of human KIAA0340 protein Authors: Inoue, K. / 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 | 2css.cif.gz | 698.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2css.ent.gz | 585.3 KB | Display | PDB format |
PDBx/mmJSON format | 2css.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/2css ftp://data.pdbj.org/pub/pdb/validation_reports/cs/2css | 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: 12698.493 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: KAZUSA cDNA hg01396 / Plasmid: P040628-04 / References: UniProt: Q86UR5 |
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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: 1.33mM U-15N,13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O 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 |
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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 |