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Yorodumi- PDB-1pdr: CRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN FROM THE HUMAN HOMOLOG ... -
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-Basic information
Entry | Database: PDB / ID: 1pdr | ||||||
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Title | CRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN FROM THE HUMAN HOMOLOG OF DISCS LARGE PROTEIN | ||||||
Components | HUMAN DISCS LARGE PROTEIN | ||||||
Keywords | SIGNAL TRANSDUCTION / SH3 DOMAIN | ||||||
Function / homology | Function and homology information regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade ...regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade / guanylate kinase activity / cortical microtubule organization / regulation of sodium ion transmembrane transport / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / NrCAM interactions / lateral loop / reproductive structure development / immunological synapse formation / myelin sheath abaxonal region / receptor localization to synapse / peristalsis / cell projection membrane / Synaptic adhesion-like molecules / smooth muscle tissue development / bicellular tight junction assembly / positive regulation of potassium ion transport / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / Trafficking of AMPA receptors / protein-containing complex localization / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / amyloid precursor protein metabolic process / lens development in camera-type eye / endothelial cell proliferation / Activation of Ca-permeable Kainate Receptor / regulation of myelination / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / establishment or maintenance of cell polarity / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / Negative regulation of NMDA receptor-mediated neuronal transmission / receptor clustering / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane neurotransmitter receptor levels / phosphoprotein phosphatase activity / Long-term potentiation / immunological synapse / intercalated disc / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / basement membrane / lateral plasma membrane / potassium channel regulator activity / bicellular tight junction / phosphatase binding / negative regulation of T cell proliferation / T cell proliferation / cytoskeletal protein binding / ionotropic glutamate receptor binding / Ras activation upon Ca2+ influx through NMDA receptor / actin filament polymerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of membrane potential / synaptic membrane / actin filament organization / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / adherens junction / postsynaptic density membrane / neuromuscular junction / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade / sarcolemma / cell-cell adhesion / negative regulation of epithelial cell proliferation / cell-cell junction / cell junction / regulation of cell shape / RAF/MAP kinase cascade / chemical synaptic transmission / basolateral plasma membrane / transmembrane transporter binding / microtubule / molecular adaptor activity / neuron projection / cadherin binding / apical plasma membrane / membrane raft / glutamatergic synapse / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Cabral, J.M. / Liddington, R. | ||||||
Citation | Journal: Nature / Year: 1996 Title: Crystal structure of a PDZ domain. Authors: Morais Cabral, J.H. / Petosa, C. / Sutcliffe, M.J. / Raza, S. / Byron, O. / Poy, F. / Marfatia, S.M. / Chishti, A.H. / Liddington, R.C. #1: Journal: Cell(Cambridge,Mass.) / Year: 1996 Title: Clustering Membrane Proteins: It'S All Coming Together with the Psd-95/Sap90 Protein Family Authors: Gomperts, S.N. #2: Journal: Trends Biochem.Sci. / Year: 1995 Title: Dhr Domains in Syntrophins, Neuronal No Synthases and Other Intracellular Proteins Authors: Ponting, C.P. / Phillips, C. #3: Journal: Nature / Year: 1995 Title: Clustering of Shaker-Type K+ Channels by Interaction with a Family of Membrane-Associated Guanylate Kinases Authors: Kim, E. / Niethammer, M. / Rothschild, A. / Jan, Y.N. / Sheng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pdr.cif.gz | 32.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pdr.ent.gz | 22.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/1pdr ftp://data.pdbj.org/pub/pdb/validation_reports/pd/1pdr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 10556.708 Da / Num. of mol.: 1 / Fragment: PDZ3 DOMAIN, DHR3 DOMAIN Source method: isolated from a genetically manipulated source Details: THE THIRD PDZ DOMAIN OF THE HUMAN HOMOLOGUE OF DISCS LARGE PROTEIN Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q12959 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.26 Å3/Da / Density % sol: 76.61 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.5 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 12, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 5911 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.108 |
Reflection | *PLUS Highest resolution: 2.8 Å |
Reflection shell | *PLUS Rmerge(I) obs: 0.301 |
-Processing
Software |
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Refinement | Resolution: 2.8→10 Å / σ(F): 2 Details: SER 517 IS POSITIONED IN A VERY TIGHT LOOP AND THERE IS CLEAR DENSITY FOR ITS MAIN CHAIN ATOMS. THE PHI AND PSI ANGLES FOR THIS RESIDUE ARE OUTSIDE THE EXPECTED RANGE. THE DEPOSITORS ...Details: SER 517 IS POSITIONED IN A VERY TIGHT LOOP AND THERE IS CLEAR DENSITY FOR ITS MAIN CHAIN ATOMS. THE PHI AND PSI ANGLES FOR THIS RESIDUE ARE OUTSIDE THE EXPECTED RANGE. THE DEPOSITORS ATTEMPTED REPEATEDLY TO REGULARIZE THEM BUT THEY ALWAYS REFINED TO THE SAME VALUES.
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Displacement parameters | Biso mean: 16.7 Å2 | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | |||||||||||||||
Refinement | *PLUS | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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