+Open data
-Basic information
Entry | Database: PDB / ID: 3x23 | ||||||
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Title | Radixin complex | ||||||
Components |
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Keywords | CELL INVASION / FERM domain / Cell adhesion / Adhesion receptors | ||||||
Function / homology | Function and homology information membrane-type matrix metalloproteinase-1 / negative regulation of homotypic cell-cell adhesion / craniofacial suture morphogenesis / regulation of actin filament bundle assembly / positive regulation of macrophage migration / macropinosome / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / response to odorant ...membrane-type matrix metalloproteinase-1 / negative regulation of homotypic cell-cell adhesion / craniofacial suture morphogenesis / regulation of actin filament bundle assembly / positive regulation of macrophage migration / macropinosome / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / response to odorant / microvillus assembly / head development / chondrocyte proliferation / negative regulation of adherens junction organization / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction / cell tip / tissue remodeling / Recycling pathway of L1 / astrocyte cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein localization to early endosome / negative regulation of focal adhesion assembly / positive regulation of protein processing / stereocilium / endochondral ossification / apical protein localization / barbed-end actin filament capping / negative regulation of cell size / embryonic cranial skeleton morphogenesis / establishment of endothelial barrier / endothelial cell proliferation / cellular response to thyroid hormone stimulus / zymogen activation / intermediate filament cytoskeleton / protein kinase A binding / positive regulation of B cell differentiation / regulation of cell size / cortical actin cytoskeleton / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / negative regulation of Notch signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / metalloaminopeptidase activity / cleavage furrow / microvillus / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / positive regulation of G1/S transition of mitotic cell cycle / regulation of protein localization to plasma membrane / response to mechanical stimulus / protein kinase A signaling / ovarian follicle development / ruffle / T-tubule / extracellular matrix / Degradation of the extracellular matrix / cell adhesion molecule binding / extracellular matrix organization / filopodium / skeletal system development / cell motility / cell periphery / protein localization to plasma membrane / adherens junction / lung development / establishment of protein localization / metalloendopeptidase activity / response to organic cyclic compound / protein processing / Golgi lumen / response to estrogen / male gonad development / positive regulation of protein catabolic process / melanosome / integrin binding / apical part of cell / lamellipodium / myelin sheath / actin binding / midbody / ATPase binding / regulation of cell shape / cytoplasmic vesicle / positive regulation of cell growth / angiogenesis / endopeptidase activity / response to oxidative stress / response to hypoxia / positive regulation of cell migration / apical plasma membrane / protein domain specific binding / serine-type endopeptidase activity / focal adhesion / positive regulation of gene expression / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å | ||||||
Authors | Terawaki, S. / Kitano, K. / Aoyama, M. / Mori, T. / Hakoshima, T. | ||||||
Citation | Journal: Genes Cells / Year: 2015 Title: MT1-MMP recognition by ERM proteins and its implication in CD44 shedding Authors: Terawaki, S. / Kitano, K. / Aoyama, M. / Mori, T. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x23.cif.gz | 149 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x23.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 3x23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/3x23 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/3x23 | 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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Unit cell |
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-Components
#1: Protein | Mass: 36924.559 Da / Num. of mol.: 1 / Fragment: FERM domain, UNP reisudes 1-310 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rdx / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P26043 |
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#2: Protein/peptide | Mass: 2474.954 Da / Num. of mol.: 1 / Fragment: cytoplasmic tail, UNP residues 563-582 / Source method: obtained synthetically / Details: human / Source: (synth.) Homo sapiens (human) / References: UniProt: P50281 |
#3: 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: 3.53 Å3/Da / Density % sol: 65.2 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12% polyethylene glycol 4000, 100mM MOPS (pH 7.0), 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2006 |
Radiation | Monochromator: Fixed exit Si (111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.396→19.833 Å / Num. obs: 22917 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.045 |
Reflection shell | Resolution: 2.4→2.47 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GC7 Resolution: 2.396→19.833 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 26.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.396→19.833 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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