+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 / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / 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 / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation / actin crosslink formation / blood coagulation, intrinsic pathway / protein localization to bicellular tight junction / OAS antiviral response / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / positive regulation of potassium ion transmembrane transport / Cell-extracellular matrix interactions / early endosome to late endosome transport / apical dendrite / Fc-gamma receptor I complex binding / cell-cell junction organization / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / protein localization to cell surface / wound healing, spreading of cells / negative regulation of transcription by RNA polymerase I / megakaryocyte development / GP1b-IX-V activation signalling / cortical cytoskeleton / positive regulation of axon regeneration / receptor clustering / SMAD binding / RHO GTPases activate PAKs / actin filament bundle / brush border / semaphorin-plexin signaling pathway / mitotic spindle assembly / cilium 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 / release of sequestered calcium ion into cytosol / regulation of cell migration / dendritic shaft / protein localization to plasma membrane / G protein-coupled receptor binding / actin filament / protein kinase C binding / synapse organization / mRNA transcription by RNA polymerase II / establishment of protein localization / trans-Golgi network / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / cerebral cortex development / small GTPase binding / kinase binding / platelet aggregation / Z disc / positive regulation of protein import into nucleus / cell-cell junction / actin filament binding / actin cytoskeleton / Platelet degranulation / GTPase binding / negative regulation of neuron projection development / actin cytoskeleton organization / postsynapse / perikaryon / angiogenesis / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / 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 / cytoplasm / cytosol 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
Summary document | 2j3s_validation.pdf.gz | 465.9 KB | Display | wwPDB validaton report |
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Full document | 2j3s_full_validation.pdf.gz | 474.9 KB | Display | |
Data in XML | 2j3s_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 2j3s_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/2j3s ftp://data.pdbj.org/pub/pdb/validation_reports/j3/2j3s | HTTPS FTP |
-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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