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Yorodumi- PDB-2l6h: Fat domain of focal adhesion kinase tethered to LD4 motif of paxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l6h | ||||||
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Title | Fat domain of focal adhesion kinase tethered to LD4 motif of paxillin via GGS linker | ||||||
Components | Focal adhesion kinase 1, linker, Paxillin | ||||||
Keywords | TRANSFERASE / CELL ADHESION / FAT / FAK / LD4 / LD2 / PAXILLIN / Fusion protein / Chimera protein | ||||||
Function / homology | Function and homology information Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / vinculin binding ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / vinculin binding / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / angiogenesis involved in wound healing / signal complex assembly / response to pH / negative regulation of cell-substrate adhesion / wound healing, spreading of cells / positive regulation of focal adhesion assembly / positive regulation of protein tyrosine kinase activity / negative regulation of anoikis / endothelial cell migration / regulation of cell adhesion / stress fiber / response to muscle stretch / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / ciliary basal body / molecular function activator activity / actin filament organization / epidermal growth factor receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / sarcolemma / integrin binding / positive regulation of protein binding / cell cortex / protein tyrosine kinase activity / protease binding / protein autophosphorylation / dendritic spine / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) unidentified (others) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Bertolucci, C.M. / Guibao, C. / Zhang, C. / Zheng, J. | ||||||
Citation | Journal: To be Published Title: Fat Domain of Focal Adhesion Kinase Tethered to Ld4 Motif of Paxillin via GGS Linker Authors: Bertolucci, C.M. / Guibao, C. / Zheng, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l6h.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2l6h.ent.gz | 940.6 KB | Display | PDB format |
PDBx/mmJSON format | 2l6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2l6h_validation.pdf.gz | 348.8 KB | Display | wwPDB validaton report |
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Full document | 2l6h_full_validation.pdf.gz | 525.4 KB | Display | |
Data in XML | 2l6h_validation.xml.gz | 61 KB | Display | |
Data in CIF | 2l6h_validation.cif.gz | 74.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/2l6h ftp://data.pdbj.org/pub/pdb/validation_reports/l6/2l6h | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 18949.475 Da / Num. of mol.: 1 Fragment: FAT DOMAIN, UNP RESIDUES 916-1053, LINKER, LD4, UNP RESIDUES 262-276 Source method: isolated from a genetically manipulated source Details: Fat domain of focal adhesion kinase with the Ld4 motif of paxillin tethered via linker GSGSGSGSGGSGGSGGSGGSGGSGGS Source: (gene. exp.) Gallus gallus, unidentified / Gene: PTK2, FAK, FAK1, PXN / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q00944, UniProt: P49024, non-specific protein-tyrosine kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 5 mM LD2 FROM PAXILLIN-4, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 10 / pH: 6.5 / Pressure: AMBIENT Pa / Temperature: 310 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS / Software ordinal: 1 Details: THE SAMPLES USED ARE CONSTRUCTS IN WHICH ONE MOTIF IS TETHERED TO THE C-TERMINUS OF THE FAT DOMAIN VIA A GGSX LINKER AND THE OTHER LD MOTIF IS BOUND AS A FREE PEPTIDE. THE GGS LINKERS ARE ...Details: THE SAMPLES USED ARE CONSTRUCTS IN WHICH ONE MOTIF IS TETHERED TO THE C-TERMINUS OF THE FAT DOMAIN VIA A GGSX LINKER AND THE OTHER LD MOTIF IS BOUND AS A FREE PEPTIDE. THE GGS LINKERS ARE UNSTRUCTURED AND COMPARISON OF SPECTRA LEAD US TO BELIEVE THEY DO NOT IMPOSE ANY CONSTRAINT UPON HOW THE TETHERED LD MOTIFS BIND TO FAT. HOWEVER WHEN ANALYZING THE STRUCTURE IN CYANA, THE PRESENCE OF THE GGS LINKER IN THE SEQUENCE INTERFERS WITH CYANA'S INITIAL ALIGNMENT OF THE 20 LOWEST ENERGY STRUCTURES AND THUS CONFUSES RMSD AND TARGET FUNCTION CALCULATIONS. WE FOUND THAT USING PSEUDO LINKERS IN CYANA RESOLVED THIS PROBLEM WITHOUT CHANGING THE STRUCTURES IN QUESTION AND SO WE CHOSE TO SUBMIT THE STRUCTURES IN THAT WAY. 2RP6 REPRESENTS A COMPOSITE STRUCTURE USING CONSTRAINTS OBTAINED FROM THE 2RP7 AND 2RP9 DATA SETS. IT DOES NOT REPRESENT A NEW CONSTRUCT IN ITSELF, BUT MOST ACCURATELY REPRESENTS THE COMPLETE COMPLEX STRUCTURE BETWEEN PAXILLIN AND FOCAL ADHESION KINASE. | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20 |