+Open data
-Basic information
Entry | Database: PDB / ID: 2j3s | ||||||
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Title | Crystal structure of the human filamin A Ig domains 19 to 21 | ||||||
Components | FILAMIN-A | ||||||
Keywords | STRUCTURAL PROTEIN / CYTOSKELETON / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information 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 / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation ...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 / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation / actin crosslink formation / OAS antiviral response / blood coagulation, intrinsic pathway / protein localization to bicellular tight junction / positive regulation of actin filament bundle assembly / 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 / negative regulation of transcription by RNA polymerase I / Fc-gamma receptor I complex binding / wound healing, spreading of cells / megakaryocyte development / GP1b-IX-V activation signalling / cortical cytoskeleton / receptor clustering / positive regulation of axon regeneration / actin filament bundle / SMAD binding / RHO GTPases activate PAKs / brush border / semaphorin-plexin signaling pathway / cilium assembly / mitotic spindle assembly / potassium channel regulator activity / epithelial to mesenchymal transition / blood vessel remodeling / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / release of sequestered calcium ion into cytosol / protein kinase C binding / dendritic shaft / G protein-coupled receptor binding / actin filament / protein localization to plasma membrane / synapse organization / 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 / cerebral cortex development / platelet aggregation / small GTPase binding / Z disc / kinase binding / positive regulation of protein import into nucleus / actin filament binding / cell-cell junction / actin cytoskeleton / negative regulation of neuron projection development / Platelet degranulation / GTPase binding / perikaryon / actin cytoskeleton organization / postsynapse / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor binding / transmembrane transporter binding / protein stabilization / cadherin binding / focal adhesion / glutamatergic synapse / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kiema, T.-R. / Ylanne, J. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Structure of Three Tandem Filamin Domains Reveals Auto-Inhibition of Ligand-Binding. Authors: Lad, Y. / Kiema, T.-R. / Jiang, P. / Pentikanen, O.T. / Coles, C.H. / Campbell, I.D. / Calderwood, D.A. / Ylanne, J. | ||||||
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 | 2j3s.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j3s.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 2j3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/2j3s ftp://data.pdbj.org/pub/pdb/validation_reports/j3/2j3s | HTTPS FTP |
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-Related structure data
Related structure data | 1v05S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 30595.975 Da / Num. of mol.: 2 Fragment: IMMUNOGLOBULIN-LIKE DOMAINS 19 TO 21, RESIDUES 2045-2329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21333 #2: Chemical | #3: Chemical | ChemComp-DIO / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Sequence details | THE THREE N-TERMINAL RESIDUES GLY ALA MET ORIGINATE FROM THE EXPRESSION | |
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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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 6.1 Details: PROTEIN WAS CRYSTALLIZED FROM 1.6M AMMONIUM SULPHATE, 0.1M CITRIC ACID PH 6.1, 10% DIOXANE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91975 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 4, 2004 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91975 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→43.44 Å / Num. obs: 22693 / % possible obs: 99 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V05 Resolution: 2.5→43.44 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.85 / SU B: 22.911 / SU ML: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDECHAIN ATOMS OF RESIDUES A 2051 ARG, A 2059 GLU, A 2074 ASP, A 2077 TYR, A 2089 LYS, A 2098 GLU, A 2123 GLN, A 2177 GLN, A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDECHAIN ATOMS OF RESIDUES A 2051 ARG, A 2059 GLU, A 2074 ASP, A 2077 TYR, A 2089 LYS, A 2098 GLU, A 2123 GLN, A 2177 GLN, A 2187 GLU, A 2289 LYS B 2051 ARG, B 2058 HIS, B 2077 TYR, B 2098 GLU, B 2133 LYS, B2137 GLU, B 2149 ARG, B 2201 ARG, B 2202 PHE, B 2203 VAL, B 2206 GLU, B 2212 VAL, B 2228 PHE, B 2239 HIS, B 2240 LYS, B2280 LYS, B 2282 GLU, B 2289 LYS, B2290 ASP, B 2311 PHE AND B 2314 GLU HAVE A POORLY DEFINED ELECTRON DENSITY.
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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: 34.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→43.44 Å
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Refine LS restraints |
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