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Yorodumi- PDB-2d11: Crystal structure of the Radixin FERM domain complexed with the N... -
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-Basic information
Entry | Database: PDB / ID: 2d11 | ||||||
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Title | Crystal structure of the Radixin FERM domain complexed with the NHERF-2 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 / regulation of actin filament bundle assembly / type 2 metabotropic glutamate receptor binding / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / microvillus assembly / negative regulation of adherens junction organization / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction ...negative regulation of homotypic cell-cell adhesion / regulation of actin filament bundle assembly / type 2 metabotropic glutamate receptor binding / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / microvillus assembly / negative regulation of adherens junction organization / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction / cell tip / Recycling pathway of L1 / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein localization to early endosome / stereocilium / type 3 metabotropic glutamate receptor binding / apical protein localization / barbed-end actin filament capping / negative regulation of cell size / establishment of endothelial barrier / cellular response to thyroid hormone stimulus / protein kinase A binding / regulation of cell size / cortical actin cytoskeleton / cleavage furrow / microvillus / positive regulation of G1/S transition of mitotic cell cycle / phosphatase binding / endomembrane system / protein-membrane adaptor activity / protein kinase A signaling / ruffle / T-tubule / cell adhesion molecule binding / filopodium / cell periphery / protein localization to plasma membrane / adherens junction / establishment of protein localization / beta-catenin binding / positive regulation of protein catabolic process / apical part of cell / lamellipodium / myelin sheath / actin binding / midbody / ATPase binding / regulation of cell shape / protein-containing complex assembly / positive regulation of cell migration / cadherin binding / apical plasma membrane / protein domain specific binding / signaling receptor binding / focal adhesion / positive regulation of gene expression / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 | 2d11.cif.gz | 260.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d11.ent.gz | 212.7 KB | Display | PDB format |
PDBx/mmJSON format | 2d11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/2d11 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/2d11 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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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 1-310) 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: 3517.120 Da / Num. of mol.: 4 / Fragment: residues 310-337 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: Q15599 #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: 2.6 Å3/Da / Density % sol: 53 % |
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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: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 118872 / Num. obs: 41789 / % possible obs: 95 % |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→29.7 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.862 / SU B: 15.9 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / 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: 36.403 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→29.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.806→2.878 Å / Total num. of bins used: 20
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