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Yorodumi- PDB-2jf1: CRYSTAL STRUCTURE OF THE FILAMIN A REPEAT 21 COMPLEXED WITH THE I... -
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-Basic information
Entry | Database: PDB / ID: 2jf1 | ||||||
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Title | CRYSTAL STRUCTURE OF THE FILAMIN A REPEAT 21 COMPLEXED WITH THE INTEGRIN BETA2 CYTOPLASMIC TAIL PEPTIDE | ||||||
Components |
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Keywords | CELL ADHESION / ACTIN-BINDING / TRANSMEMBRANE / ACETYLATION / POLYMORPHISM / CYTOSKELETON / GLYCOPROTEIN / FILAMIN / COMPLEX / MEMBRANE / INTEGRIN / RECEPTOR / PYRROLIDONE CARBOXYLIC ACID / PHOSPHORYLATION / DISEASE MUTATION / IMMUNOGLOBULIN LIKE | ||||||
Function / homology | Function and homology information integrin alphaX-beta2 complex / regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / establishment of Sertoli cell barrier / Myb complex / formation of radial glial scaffolds / integrin alphaM-beta2 complex / glycoprotein Ib-IX-V complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation ...integrin alphaX-beta2 complex / regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / establishment of Sertoli cell barrier / Myb complex / formation of radial glial scaffolds / integrin alphaM-beta2 complex / glycoprotein Ib-IX-V complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / adenylate cyclase-inhibiting dopamine receptor signaling pathway / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation / actin crosslink formation / OAS antiviral response / blood coagulation, intrinsic pathway / complement component C3b binding / protein localization to bicellular tight junction / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / positive regulation of actin filament bundle assembly / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of neuron migration / Cell-extracellular matrix interactions / positive regulation of potassium ion transmembrane transport / early endosome to late endosome transport / apical dendrite / cell-cell junction organization / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / protein localization to cell surface / heterotypic cell-cell adhesion / integrin complex / negative regulation of transcription by RNA polymerase I / Fc-gamma receptor I complex binding / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / megakaryocyte development / leukocyte cell-cell adhesion / phagocytosis, engulfment / GP1b-IX-V activation signalling / cortical cytoskeleton / receptor clustering / endodermal cell differentiation / positive regulation of axon regeneration / amyloid-beta clearance / actin filament bundle / SMAD binding / RHO GTPases activate PAKs / plasma membrane raft / tertiary granule membrane / brush border / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / cilium assembly / mitotic spindle assembly / positive regulation of protein targeting to membrane / potassium channel regulator activity / epithelial to mesenchymal transition / blood vessel remodeling / Integrin cell surface interactions / specific granule membrane / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / regulation of peptidyl-tyrosine phosphorylation / release of sequestered calcium ion into cytosol / heat shock protein binding / receptor-mediated endocytosis / cell adhesion molecule binding / cell-matrix adhesion / neutrophil chemotaxis / protein kinase C binding / positive regulation of superoxide anion generation / dendritic shaft / G protein-coupled receptor binding / actin filament / integrin-mediated signaling pathway / protein localization to plasma membrane / Cell surface interactions at the vascular wall / synapse organization / microglial cell activation / mRNA transcription by RNA polymerase II / establishment of protein localization / trans-Golgi network / negative regulation of DNA-binding transcription factor activity / negative regulation of protein catabolic process / receptor internalization / cell-cell adhesion / cerebral cortex development / platelet aggregation / Z disc / small GTPase binding / kinase binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kiema, T. / Ylanne, J. | ||||||
Citation | Journal: Blood / Year: 2008 Title: Beta2 Integrin Phosphorylation on Thr758 Acts as a Molecular Switch to Regulate 14-3-3 and Filamin Binding. Authors: Takala, H. / Nurminen, E. / Nurmi, S.M. / Aatonen, M. / Strandin, T. / Takatalo, M. / Kiema, T. / Gahmberg, C.G. / Ylanne, J. / Fagerholm, S.C. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jf1.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jf1.ent.gz | 21.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/2jf1 ftp://data.pdbj.org/pub/pdb/validation_reports/jf/2jf1 | HTTPS FTP |
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-Related structure data
Related structure data | 2v7dC 2brqS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9964.994 Da / Num. of mol.: 1 / Fragment: IG 21, RESIDUES 2236-2329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P21333 |
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#2: Protein/peptide | Mass: 4213.747 Da / Num. of mol.: 1 / Fragment: RESIDUES 735-769 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05107 |
#3: Chemical | ChemComp-GOL / |
#4: 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: 3.91 Å3/Da / Density % sol: 68.32 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 1.6-1.58 M AMMONIUM SULPHATE, 0.1 M NA-ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 25, 2005 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.46 Å / Num. obs: 8482 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 6.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BRQ Resolution: 2.2→45.45 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.77 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.197 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→45.45 Å
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