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Yorodumi- PDB-2yvc: Crystal structure of the Radixin FERM domain complexed with the N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yvc | ||||||
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Title | Crystal structure of the Radixin FERM domain complexed with the NEP cytoplasmic tail | ||||||
Components |
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Keywords | CELL ADHESION / Protein-peptide complex | ||||||
Function / homology | Function and homology information negative regulation of homotypic cell-cell adhesion / neuropeptide processing / neprilysin / creatinine metabolic process / regulation of actin filament bundle assembly / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / Metabolism of Angiotensinogen to Angiotensins / oligopeptidase activity ...negative regulation of homotypic cell-cell adhesion / neuropeptide processing / neprilysin / creatinine metabolic process / regulation of actin filament bundle assembly / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / Metabolism of Angiotensinogen to Angiotensins / oligopeptidase activity / microvillus assembly / negative regulation of adherens junction organization / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction / exopeptidase activity / cell tip / Recycling pathway of L1 / peptide metabolic process / cellular response to UV-A / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein localization to early endosome / amyloid-beta clearance by cellular catabolic process / cardiolipin binding / stereocilium / apical protein localization / barbed-end actin filament capping / neuron projection terminus / negative regulation of cell size / establishment of endothelial barrier / cellular response to thyroid hormone stimulus / protein kinase A binding / positive regulation of neurogenesis / regulation of cell size / cortical actin cytoskeleton / phosphatidylserine binding / cellular response to UV-B / amyloid-beta clearance / cellular response to cytokine stimulus / cleavage furrow / microvillus / brush border / replicative senescence / positive regulation of G1/S transition of mitotic cell cycle / amyloid-beta metabolic process / protein kinase A signaling / sensory perception of pain / ruffle / T-tubule / Neutrophil degranulation / cell adhesion molecule binding / filopodium / placenta development / kidney development / positive regulation of long-term synaptic potentiation / cell periphery / protein localization to plasma membrane / adherens junction / peptide binding / lung development / establishment of protein localization / trans-Golgi network / metalloendopeptidase activity / positive regulation of protein catabolic process / metallopeptidase activity / synaptic vesicle / presynapse / apical part of cell / lamellipodium / myelin sheath / actin binding / peptidase activity / midbody / ATPase binding / regulation of cell shape / cytoplasmic vesicle / endopeptidase activity / membrane => GO:0016020 / learning or memory / early endosome / positive regulation of cell migration / membrane raft / apical plasma membrane / axon / protein domain specific binding / dendrite / neuronal cell body / synapse / positive regulation of gene expression / protein homodimerization activity / proteolysis / zinc ion binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Terawaki, S. / Kitano, K. / Hakoshima, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural basis for type II membrane protein binding by ERM proteins revealed by the radixin-neutral endopeptidase 24.11 (NEP) complex Authors: Terawaki, S. / Kitano, K. / Hakoshima, T. #1: 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. #2: 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. #3: Journal: Structure / Year: 2006 Title: Structural basis for NHERF recognition by ERM proteins Authors: Terawaki, S. / Maesaki, R. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yvc.cif.gz | 357 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yvc.ent.gz | 294.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yvc ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yvc | HTTPS FTP |
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-Related structure data
Related structure data | 1gc7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 36924.559 Da / Num. of mol.: 3 / Fragment: FERM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P26043 #2: Protein/peptide | Mass: 2533.902 Da / Num. of mol.: 3 / Fragment: cytoplasmic tail / Source method: obtained synthetically / Details: This sequence occurs naturally in mouse. / References: UniProt: Q61391 |
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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: 3.81 Å3/Da / Density % sol: 67.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG3350, 0.2M DL-maleic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2005 |
Radiation | Monochromator: rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→29.71 Å / Num. obs: 30656 / % possible obs: 99.7 % |
Reflection shell | Resolution: 3.2→3.31 Å / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GC7 Resolution: 3.2→29.71 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.876 / SU B: 45.646 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / 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: 64.391 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.195→3.277 Å / Total num. of bins used: 20
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