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- PDB-1qvx: SOLUTION STRUCTURE OF THE FAT DOMAIN OF FOCAL ADHESION KINASE -

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Basic information

Entry
Database: PDB / ID: 1qvx
TitleSOLUTION STRUCTURE OF THE FAT DOMAIN OF FOCAL ADHESION KINASE
ComponentsFocal adhesion kinase 1PTK2
KeywordsTRANSFERASE / FOCAL ADHESION KINASE / FAK / FOCAL ADHENSION TARGETING DOMAIN / FAT / HELIX BUNDLE
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 / Integrin signaling ...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 / 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 / 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 / negative regulation of anoikis / positive regulation of protein tyrosine kinase activity / regulation of cell adhesion / response to muscle stretch / ciliary basal body / actin filament organization / molecular function activator activity / sarcolemma / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / integrin binding / cell cortex / positive regulation of protein binding / angiogenesis / protein tyrosine kinase activity / protease binding / dendritic spine / protein autophosphorylation / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation / perinuclear region of cytoplasm / ATP binding / nucleus / identical protein binding / cytoplasm
Similarity search - Function
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. ...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 / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / The program CNS version 1.1 with ARIA version 1.2 module was used to calculate the structures of the avian FAT domain.
AuthorsGao, G. / Prutzman, K.C. / King, M.L. / DeRose, E.F. / London, R.E. / Schaller, M.D. / Campbell, S.L.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: NMR Solution Structure of the Focal Adhesion Targeting Domain of Focal Adhesion Kinase in Complex with a Paxillin LD Peptide: EVIDENCE FOR A TWO-SITE BINDING MODEL.
Authors: Gao, G. / Prutzman, K.C. / King, M.L. / Scheswohl, D.M. / DeRose, E.F. / London, R.E. / Schaller, M.D. / Campbell, S.L.
History
DepositionAug 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 5, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_representative / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_torsion
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_nmr_representative.conformer_id / _pdbx_nmr_software.name / _pdbx_validate_close_contact.PDB_model_num / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_peptide_omega.PDB_model_num / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Revision 2.1Jun 14, 2023Group: Advisory / Database references / Other
Category: database_2 / pdbx_database_remark / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_database_status.status_code_nmr_data
Remark 650HELIX Determination method: Author determined

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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)15,0001
Polymers15,0001
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Focal adhesion kinase 1 / PTK2 / FADK 1 / PP125FAK


Mass: 15000.480 Da / Num. of mol.: 1 / Fragment: FAT DOMAIN (RESIDUES 920-1053)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: FAK / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / 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 simultaneous 13C/15N edited NOESY
1213D CBCA(CO)NH
1313D HNCA
1413D HN(CA)CB
1513D H(CCO)-TOCSY-NNH
1613D (H)C(CO)-TOCSY-NNH
NMR detailsText: Aromatic sidechain assignments were obtained from 2D (HB)CB(CGCDCE)HE and 2D (HB)CB(CGCD)HD experiments. 1H-15N residual dipolar coupling values were measured using 7.5 mg/ml Pf1 phage as aligning medium

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Sample preparation

DetailsContents: 0.6mM 13C,15N labeled FAT with 4.8mM LD2 peptide, 25mM TRIS-MALEATE, 0.1% NAN3, 1.0uM PPACK, 0.5mg/mL PEFABLOC, 90% H2O, 10% D2O
Solvent system: 20mM deuterated Tris-maleate, 50mM NaCl, 0.1mM EDTA, 0.1% NaN3, and 10% D2O, pH 6.0
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.0 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T. et al.refinement
NMRPipe2.1Delaglio, F. et al.processing
VNMR6.1Variancollection
ARIA1.2Linge, J.P. et al.refinement
NMRView5.0.4Johnson, B.A. et al.data analysis
RefinementMethod: The program CNS version 1.1 with ARIA version 1.2 module was used to calculate the structures of the avian FAT domain.
Software ordinal: 1
Details: The structural restraints included NOE, hydrogen bond, dihedral angle, and RDC restraints. The NOE distance restraints were derived from a 3D simultaneous 13C/15N edited NOESY peak lists ...Details: The structural restraints included NOE, hydrogen bond, dihedral angle, and RDC restraints. The NOE distance restraints were derived from a 3D simultaneous 13C/15N edited NOESY peak lists with 75 ms mixing time. The peak lists were generated automatically by NMRView and edited manually to remove any obvious water and apodization artifacts. The peak lists were unassigned and uncalibrated with respect to distance. To calibrate the NOE distances, the rotational correlation time of the complex was set to 10 ns and was based on values obtained on proteins of this size at similar temperature. The default parameters for ARIA produced structures with poor convergence. Several parameters were optimized, including the ambiguous cutoff (rho), the violation tolerance (vtol), and maximum number of ambiguities per peak (maxn), to provide better noise discrimination. The following scheme led to the best convergence over 9 iterations: rho = (0.95, 0.95, 0.95, 0.94, 0.93, 0.92, 0.91, 0.90, 0 80), vtol = (5.0, 2.0, 1.0, 0.5, 0.25, 1.0, 0.1, 0.1, 0.1), maxn = 5 for all iterations. An ensemble of 25 calculated NMR structures of the avian FAT domain was selected for further analysis.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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