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Yorodumi- PDB-5f28: Crystal structure of FAT domain of Focal Adhesion Kinase (FAK) bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f28 | ||||||
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Title | Crystal structure of FAT domain of Focal Adhesion Kinase (FAK) bound to the transcription factor MEF2C | ||||||
Components |
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Keywords | Transcription / protein binding / Transcription Factor / Kinase / Cardiovascular disease | ||||||
Function / homology | Function and homology information primary heart field specification / sinoatrial valve morphogenesis / positive regulation of alkaline phosphatase activity / nephron tubule epithelial cell differentiation / muscle cell fate determination / regulation of sarcomere organization / cardiac ventricle formation / cartilage morphogenesis / glomerulus morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis ...primary heart field specification / sinoatrial valve morphogenesis / positive regulation of alkaline phosphatase activity / nephron tubule epithelial cell differentiation / muscle cell fate determination / regulation of sarcomere organization / cardiac ventricle formation / cartilage morphogenesis / glomerulus morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / positive regulation of skeletal muscle cell differentiation / DCC mediated attractive signaling / positive regulation of macrophage apoptotic process / Apoptotic cleavage of cellular proteins / DNA-binding transcription factor binding => GO:0140297 / MET activates PTK2 signaling / transdifferentiation / HMG box domain binding / NCAM signaling for neurite out-growth / regulation of synaptic activity / secondary heart field specification / cellular response to xenobiotic stimulus => GO:0071466 / negative regulation of synapse assembly / central nervous system neuron axonogenesis / renal tubule morphogenesis / cellular response to trichostatin A / cell morphogenesis involved in neuron differentiation / EPHB-mediated forward signaling / ventricular cardiac muscle cell differentiation / positive regulation of behavioral fear response / embryonic viscerocranium morphogenesis / RHO GTPases Activate WASPs and WAVEs / positive regulation of cell proliferation in bone marrow / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of cardiac muscle cell differentiation / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Extra-nuclear estrogen signaling / RAF/MAP kinase cascade / intracellular chloride ion homeostasis / embryonic skeletal system morphogenesis / negative regulation of axonogenesis / regulation of dendritic spine development / Regulation of actin dynamics for phagocytic cup formation / negative regulation of vascular associated smooth muscle cell migration / regulation of neurotransmitter secretion / regulation of megakaryocyte differentiation / negative regulation of organ growth / positive regulation of skeletal muscle tissue development / regulation of germinal center formation / melanocyte differentiation / smooth muscle cell differentiation / regulation of modification of postsynaptic actin cytoskeleton / germinal center formation / Myogenesis / cardiac muscle cell differentiation / endochondral ossification / regulation of AMPA receptor activity / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to fluid shear stress / VEGFA-VEGFR2 Pathway / cardiac muscle hypertrophy in response to stress / signal complex assembly / negative regulation of ossification / neural crest cell differentiation / nuclear migration / regulation of NMDA receptor activity / cellular response to parathyroid hormone stimulus / negative regulation of vascular endothelial cell proliferation / platelet formation / regulation of osteoblast differentiation / regulation of synapse assembly / organ growth / roof of mouth development / positive regulation of cardiac muscle hypertrophy / blood vessel development / positive regulation of smooth muscle cell migration / B cell proliferation / heart looping / outflow tract morphogenesis / skeletal muscle cell differentiation / minor groove of adenine-thymine-rich DNA binding / negative regulation of vascular associated smooth muscle cell proliferation / regulation of cell adhesion mediated by integrin / monocyte differentiation / B cell homeostasis / humoral immune response / negative regulation of blood vessel endothelial cell migration / positive regulation of cell adhesion / intercalated disc / sarcoplasm / endothelial cell migration / neuron development / ephrin receptor signaling pathway / positive regulation of protein kinase activity / phosphatase binding / blood vessel remodeling / positive regulation of myoblast differentiation / cell fate commitment / vasculogenesis Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Cardoso, A.C. / Ambrosio, A.L.B. / Dessen, A. / Franchini, K.G. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: Structure / Year: 2016 Title: FAK Forms a Complex with MEF2 to Couple Biomechanical Signaling to Transcription in Cardiomyocytes. Authors: Cardoso, A.C. / Pereira, A.H.M. / Ambrosio, A.L.B. / Consonni, S.R. / Rocha de Oliveira, R. / Bajgelman, M.C. / Dias, S.M.G. / Franchini, K.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f28.cif.gz | 145.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f28.ent.gz | 114.1 KB | Display | PDB format |
PDBx/mmJSON format | 5f28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f28_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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Full document | 5f28_full_validation.pdf.gz | 463.9 KB | Display | |
Data in XML | 5f28_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 5f28_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/5f28 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/5f28 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 11202.983 Da / Num. of mol.: 4 / Fragment: UNP residues 1-95 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pETSUMO / Details (production host): Home-made / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q8CFN5 #2: Protein | Mass: 16531.158 Da / Num. of mol.: 3 / Fragment: UNP residues 935-1083 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: P34152 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Magnseium acetate, 0.1M MES, pH 6.5, 12% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2013 |
Radiation | Monochromator: Silicon 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.22 Å / Num. obs: 37566 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.344 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.559 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1K40 (FAT) and 3KOV (MEF2) Resolution: 2.9→43.221 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 25.04 / 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: 2.9→43.221 Å
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Refine LS restraints |
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LS refinement shell |
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