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Yorodumi- PDB-2ain: Solution structure of the AF-6 PDZ domain complexed with the C-te... -
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-Basic information
Entry | Database: PDB / ID: 2ain | ||||||
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Title | Solution structure of the AF-6 PDZ domain complexed with the C-terminal peptide from the Bcr protein | ||||||
Components |
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Keywords | CELL ADHESION/Transferase / AF-6 PDZ domain-Bcr complex / CELL ADHESION-Transferase COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of respiratory burst / negative regulation of cellular extravasation / negative regulation of macrophage migration / : / negative regulation of blood vessel remodeling / negative regulation of neutrophil degranulation / positive regulation of cell-cell adhesion mediated by cadherin / establishment of protein localization to plasma membrane / macrophage migration / neutrophil degranulation ...negative regulation of respiratory burst / negative regulation of cellular extravasation / negative regulation of macrophage migration / : / negative regulation of blood vessel remodeling / negative regulation of neutrophil degranulation / positive regulation of cell-cell adhesion mediated by cadherin / establishment of protein localization to plasma membrane / macrophage migration / neutrophil degranulation / establishment of endothelial intestinal barrier / intracellular protein transmembrane transport / positive regulation of cell-cell adhesion / pore complex assembly / cell-cell adhesion mediated by cadherin / renal system process / regulation of vascular permeability / bicellular tight junction assembly / cell-cell contact zone / regulation of Rho protein signal transduction / focal adhesion assembly / Adherens junctions interactions / definitive hemopoiesis / activation of GTPase activity / Signaling by cytosolic FGFR1 fusion mutants / tight junction / regulation of small GTPase mediated signal transduction / inner ear morphogenesis / small GTPase-mediated signal transduction / RHOB GTPase cycle / pore complex / RHOC GTPase cycle / CDC42 GTPase cycle / neuromuscular process controlling balance / homeostasis of number of cells / RHOA GTPase cycle / negative regulation of reactive oxygen species metabolic process / RAC2 GTPase cycle / RAC3 GTPase cycle / phagocytosis / positive regulation of phagocytosis / keratinocyte differentiation / RAC1 GTPase cycle / Signaling by FGFR1 in disease / cell adhesion molecule binding / GTPase activator activity / guanyl-nucleotide exchange factor activity / negative regulation of cell migration / adherens junction / brain development / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / small GTPase binding / negative regulation of inflammatory response / regulation of protein localization / actin filament binding / cell-cell junction / cell-cell signaling / cell junction / actin cytoskeleton organization / protein tyrosine kinase activity / cellular response to lipopolysaccharide / dendritic spine / postsynaptic density / regulation of cell cycle / non-specific serine/threonine protein kinase / cell adhesion / nuclear speck / cadherin binding / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / positive regulation of gene expression / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics | ||||||
Authors | Chen, Q. / Wu, J. / Shi, Y. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex. Authors: Chen, Q. / Niu, X. / Xu, Y. / Wu, J. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ain.cif.gz | 570.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ain.ent.gz | 478.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ain.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/2ain ftp://data.pdbj.org/pub/pdb/validation_reports/ai/2ain | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9566.045 Da / Num. of mol.: 1 / Fragment: AF-6 PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b (+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P55196 |
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#2: Protein/peptide | Mass: 694.773 Da / Num. of mol.: 1 / Fragment: C-terminal peptide / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. References: UniProt: P11274, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: Intermolecular interactions were identified in a 13C/15N-filtered (F1), 13C-edited(F3) 3D NOESY spectrum |
-Sample preparation
Details | Contents: 2.0mM 15N, 13C-labeled AF-6 PDZ domain, 50mM phosphate buffer (pH 5.9), 1mM EDTA, 10%(v/v) D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | pH: 5.9 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics Software ordinal: 1 Details: The complex structure is solved using a total of 1606 experimental restraints that includes 1471 intramolecular NOEs, 61 intermolecular NOEs and 74 dihedral angles restraints | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |