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Yorodumi- PDB-2d10: Crystal structure of the Radixin FERM domain complexed with the N... -
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-Basic information
Entry | Database: PDB / ID: 2d10 | ||||||
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Title | Crystal structure of the Radixin FERM domain complexed with the NHERF-1 C-terminal tail peptide | ||||||
Components |
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Keywords | CELL ADHESION / Protein-peptide complex | ||||||
Function / homology | Function and homology information negative regulation of homotypic cell-cell adhesion / dopamine receptor binding / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / regulation of actin filament bundle assembly / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / renal phosphate ion absorption ...negative regulation of homotypic cell-cell adhesion / dopamine receptor binding / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / regulation of actin filament bundle assembly / 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 / regulation of organelle assembly / cerebrospinal fluid circulation / regulation of ruffle assembly / establishment of protein localization to plasma membrane / negative regulation of sodium ion transport / microvillus assembly / positive regulation of monoatomic ion transmembrane transport / negative regulation of adherens junction organization / positive regulation of early endosome to late endosome transport / bile acid secretion / maintenance of epithelial cell apical/basal polarity / regulation of Rap protein signal transduction / intracellular phosphate ion homeostasis / cell tip / cilium organization / Recycling pathway of L1 / plasma membrane organization / stereocilium tip / gland morphogenesis / regulation of postsynaptic neurotransmitter receptor diffusion trapping / myosin II binding / phospholipase C-activating dopamine receptor signaling pathway / growth factor receptor binding / positive regulation of protein localization to early endosome / establishment of Golgi localization / fibroblast migration / stereocilium / type 3 metabotropic glutamate receptor binding / plasma membrane protein complex / apical protein localization / barbed-end actin filament capping / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / negative regulation of fibroblast migration / chloride channel regulator activity / negative regulation of platelet-derived growth factor receptor signaling pathway / establishment of endothelial barrier / cellular response to thyroid hormone stimulus / auditory receptor cell stereocilium organization / nuclear migration / regulation of protein kinase activity / beta-2 adrenergic receptor binding / protein kinase A binding / microvillus membrane / regulation of cell size / cortical actin cytoskeleton / renal absorption / cleavage furrow / microvillus / transport across blood-brain barrier / negative regulation of mitotic cell cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of G1/S transition of mitotic cell cycle / endomembrane system / phosphatase binding / protein-membrane adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / protein kinase A signaling / sperm midpiece / ruffle / T-tubule / cell adhesion molecule binding / filopodium / PDZ domain binding / cell periphery / protein localization to plasma membrane / morphogenesis of an epithelium / brush border membrane / sensory perception of sound / adherens junction / negative regulation of canonical Wnt signaling pathway / establishment of protein localization / negative regulation of ERK1 and ERK2 cascade / beta-catenin binding / Wnt signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / positive regulation of protein catabolic process / : / actin cytoskeleton / apical part of cell / lamellipodium / myelin sheath / actin binding / midbody / ATPase binding / regulation of cell shape / actin cytoskeleton organization / protein-containing complex assembly Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Terawaki, S. / Maesaki, R. / Hakoshima, T. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Structural basis for NHERF recognition by ERM proteins Authors: Terawaki, S. / Maesaki, R. / Hakoshima, T. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003 Title: Crystallographic characterization of the radixin FERM domain bound to the C-terminal region of the human Na+/H+-exchanger regulatory factor (NHERF) Authors: Terawaki, S. / Maesaki, R. / Okada, K. / Hakoshima, T. #2: Journal: Embo J. / Year: 2000 Title: Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain Authors: Hamada, K. / Shimizu, T. / Matsui, T. / Tsukita, S. / Hakoshima, T. #3: Journal: Embo J. / Year: 2003 Title: Structural basis of adhesion-molecule recognition by ERM proteins revealed by the crystal structure of the radixin-ICAM-2 complex Authors: Hamada, K. / Shimizu, T. / Yonemura, S. / Tsukita, S. / Tsukita, S. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d10.cif.gz | 274.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d10.ent.gz | 222 KB | Display | PDB format |
PDBx/mmJSON format | 2d10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/2d10 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/2d10 | HTTPS FTP |
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-Related structure data
Related structure data | 2d11C 1gc7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 36924.559 Da / Num. of mol.: 4 / Fragment: FERM domain (residues 3-312) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P26043 #2: Protein/peptide | Mass: 3409.898 Da / Num. of mol.: 4 / Fragment: residues 331-358 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: O14745 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG4000, 5% Isopropanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 62668 / Num. obs: 62668 / % possible obs: 99.2 % |
Reflection shell | Resolution: 2.5→2.64 Å / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GC7 Resolution: 2.5→29.93 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.601 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.464 / ESU R Free: 0.286 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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