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- PDB-1pv3: NMR Solution Structure of the Avian FAT-domain of Focal Adhesion ... -

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Basic information

Entry
Database: PDB / ID: 1pv3
TitleNMR Solution Structure of the Avian FAT-domain of Focal Adhesion Kinase
ComponentsFocal adhesion kinase 1
KeywordsTRANSFERASE / Focal Adhesion Kinase / Helix Bundle / FAT-Domain
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / negative regulation of protein autophosphorylation / positive regulation of protein tyrosine kinase activity / radial glia-guided pyramidal neuron migration / calcium-dependent cysteine-type endopeptidase activity ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / negative regulation of protein autophosphorylation / positive regulation of protein tyrosine kinase activity / radial glia-guided pyramidal neuron migration / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / : / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / signal complex assembly / response to pH / angiogenesis involved in wound healing / wound healing, spreading of cells / negative regulation of anoikis / positive regulation of protein binding / negative regulation of cell-substrate adhesion / positive regulation of focal adhesion assembly / regulation of cell adhesion / response to muscle stretch / molecular function activator activity / actin filament organization / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / sarcolemma / integrin binding / epidermal growth factor receptor signaling pathway / protein autophosphorylation / protease binding / protein tyrosine kinase activity / cell cortex / positive regulation of cell migration / ciliary basal body / focal adhesion / positive regulation of cell population proliferation / centrosome / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Single helix bin / Nucleotidyltransferases domain 2 / Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe ...Single helix bin / Nucleotidyltransferases domain 2 / Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Focal adhesion kinase 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsPrutzman, K.C. / Gao, G. / King, M.L. / Iyer, V.V. / Mueller, G.A. / Schaller, M.D. / Campbell, S.L.
CitationJournal: STRUCTURE / Year: 2004
Title: The Focal Adhesion Targeting Domain of Focal Adhesion Kinase Contains a Hinge Region that Modulates Tyrosine 926 Phosphorylation.
Authors: Prutzman, K.C. / Gao, G. / King, M.L. / Iyer, V.V. / Mueller, G.A. / Schaller, M.D. / Campbell, S.L.
History
DepositionJun 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 27, 2016Group: Other
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)15,8971
Polymers15,8971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 25structures with acceptable covalent geometry,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Focal adhesion kinase 1 / FADK 1 / PP125FAK


Mass: 15897.431 Da / Num. of mol.: 1 / Fragment: Focal Adhesion Targeting (FAT) Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: FAK1 OR FAK / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: Q00944, EC: 2.7.1.112

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: PDB entry 1K40 was used as a starting template for structure calculations. The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.85 mM Focal Adhesion Targeting Domain U-15N,13C, 25 mM Tris-Maleate, 0.1 % NaN3, 1.0 uM PPACK, 0.5 mg/mL Pefabloc 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 6 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Delaglio, F., Grzesiek, S., Vuister., G., Zhu, G., Pfeifer, J., Bax, A.processing
NMRView5.0.4Johnson, B., Blevins, R.A.data analysis
CNS1.1Brunger, A.T.,Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve. R.W., Jiang, J.S., Kuszewski, J., Nilges, M.,Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.structure solution
ARIA1.2Nilges, M.structure solution
ARIA1.2Nilges, M.refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: 3049 total restraints: 1627 unambiguous NOE-derived distance constraints, 1078 ambiguous NOE-derived distance constraints, 83 dihedral angle restraints, 97 distance restraints from hydrogen ...Details: 3049 total restraints: 1627 unambiguous NOE-derived distance constraints, 1078 ambiguous NOE-derived distance constraints, 83 dihedral angle restraints, 97 distance restraints from hydrogen bonds, 164 residual dipolar coupling restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 20

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