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Yorodumi- PDB-2ozf: The crystal structure of the 2nd PDZ domain of the human NHERF-1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ozf | ||||||
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Title | The crystal structure of the 2nd PDZ domain of the human NHERF-1 (SLC9A3R1) | ||||||
Components | Ezrin-radixin-moesin-binding phosphoprotein 50 | ||||||
Keywords | PROTEIN BINDING / PDZ domain / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information dopamine receptor binding / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import ...dopamine receptor binding / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / bile acid secretion / positive regulation of monoatomic ion transmembrane transport / maintenance of epithelial cell apical/basal polarity / intracellular phosphate ion homeostasis / cilium organization / plasma membrane organization / stereocilium tip / gland morphogenesis / myosin II binding / growth factor receptor binding / phospholipase C-activating dopamine receptor signaling pathway / establishment of Golgi localization / fibroblast migration / plasma membrane protein complex / type 3 metabotropic glutamate receptor binding / establishment of epithelial cell apical/basal polarity / negative regulation of fibroblast migration / chloride channel regulator activity / negative regulation of platelet-derived growth factor receptor signaling pathway / auditory receptor cell stereocilium organization / nuclear migration / regulation of protein kinase activity / beta-2 adrenergic receptor binding / microvillus membrane / regulation of cell size / renal absorption / microvillus / transport across blood-brain barrier / negative regulation of mitotic cell cycle / endomembrane system / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein-membrane adaptor activity / sperm midpiece / ruffle / positive regulation of intrinsic apoptotic signaling pathway / filopodium / PDZ domain binding / cell periphery / protein localization to plasma membrane / morphogenesis of an epithelium / sensory perception of sound / brush border membrane / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / beta-catenin binding / adenylate cyclase-activating dopamine receptor signaling pathway / protein self-association / actin cytoskeleton / regulation of cell shape / actin cytoskeleton organization / protein-containing complex assembly / vesicle / transmembrane transporter binding / apical plasma membrane / negative regulation of cell population proliferation / signaling receptor binding / protein-containing complex binding / perinuclear region of cytoplasm / extracellular exosome / membrane / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Phillips, C. / Papagrigoriou, E. / Gileadi, C. / Fedorov, O. / Elkins, J. / Berridge, G. / Turnbull, A.P. / Gileadi, O. / Schoch, G. / Smee, C. ...Phillips, C. / Papagrigoriou, E. / Gileadi, C. / Fedorov, O. / Elkins, J. / Berridge, G. / Turnbull, A.P. / Gileadi, O. / Schoch, G. / Smee, C. / Bray, J. / Savitsky, P. / Uppenberg, J. / von Delft, F. / Gorrec, F. / Umeano, C. / Salah, E. / Colebrook, S. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the 2nd PDZ domain of the human NHERF-1 (SLC9A3R1) Authors: Phillips, C. / Papagrigoriou, E. / Gileadi, C. / Fedorov, O. / Elkins, J. / Berridge, G. / Turnbull, A.P. / Gileadi, O. / Schoch, G. / Smee, C. / Bray, J. / Savitsky, P. / Uppenberg, J. / ...Authors: Phillips, C. / Papagrigoriou, E. / Gileadi, C. / Fedorov, O. / Elkins, J. / Berridge, G. / Turnbull, A.P. / Gileadi, O. / Schoch, G. / Smee, C. / Bray, J. / Savitsky, P. / Uppenberg, J. / von Delft, F. / Gorrec, F. / Umeano, C. / Salah, E. / Colebrook, S. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Doyle, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ozf.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ozf.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ozf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/2ozf ftp://data.pdbj.org/pub/pdb/validation_reports/oz/2ozf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological unit is a monomer |
-Components
#1: Protein | Mass: 9944.247 Da / Num. of mol.: 1 / Fragment: Second PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A3R1, NHERF / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14745 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M NaNO3, 0.1M BTProp, 20% PEG 3350, 10% Ethylene glycol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9183 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9183 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39.53 Å / Num. all: 18038 / Num. obs: 18038 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.601 / Num. unique all: 1826 / Rsym value: 0.5 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→39.53 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.594 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.533 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→39.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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