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- PDB-7w8b: Crystal Structure of human Focal Adhesion Targeting (FAT) domain ... -

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Basic information

Entry
Database: PDB / ID: 7w8b
TitleCrystal Structure of human Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase
ComponentsIsoform 5 of Focal adhesion kinase 1
KeywordsTRANSFERASE / Focal adhesion kinase / Protein tyrosine kinase 2
Function / homology
Function and homology information


netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of fibroblast migration / positive regulation of macrophage proliferation ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of fibroblast migration / positive regulation of macrophage proliferation / DCC mediated attractive signaling / regulation of osteoblast differentiation / growth hormone receptor signaling pathway / Signal regulatory protein family interactions / MET activates PTK2 signaling / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of focal adhesion assembly / regulation of GTPase activity / positive regulation of wound healing / establishment of cell polarity / p130Cas linkage to MAPK signaling for integrins / negative regulation of cell-cell adhesion / positive regulation of macrophage chemotaxis / positive regulation of epithelial cell migration / Apoptotic cleavage of cellular proteins / regulation of cytoskeleton organization / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / ephrin receptor signaling pathway / positive regulation of protein kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / positive regulation of epithelial to mesenchymal transition / stress fiber / EPHB-mediated forward signaling / Integrin signaling / NCAM signaling for neurite out-growth / SH2 domain binding / transforming growth factor beta receptor signaling pathway / ciliary basal body / protein tyrosine phosphatase activity / axon guidance / molecular function activator activity / integrin-mediated signaling pathway / cell motility / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / regulation of protein phosphorylation / epidermal growth factor receptor signaling pathway / placenta development / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / integrin binding / cell migration / regulation of cell shape / regulation of cell population proliferation / actin binding / cell cortex / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein phosphatase binding / angiogenesis / protein autophosphorylation / Extra-nuclear estrogen signaling / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / focal adhesion / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / PH-like domain superfamily / 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
Similarity search - Domain/homology
Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.093 Å
AuthorsMomin, A.A. / Sandholu, A.S. / Arold, S.T.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
King Abdullah University of Science and TechnologyURF/1/2602-01-01 Saudi Arabia
CitationJournal: To Be Published
Title: Crystal Structure of human Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase
Authors: Momin, A.A. / Sandholu, A.S. / Arold, S.T.
History
DepositionDec 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 5 of Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)18,2771
Polymers18,2771
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10950 Å2
Unit cell
Length a, b, c (Å)39.333, 94.311, 85.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1101-

HOH

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Components

#1: Protein Isoform 5 of Focal adhesion kinase 1 / FADK 1 / Focal adhesion kinase-related nonkinase / FRNK / Protein phosphatase 1 regulatory subunit ...FADK 1 / Focal adhesion kinase-related nonkinase / FRNK / Protein phosphatase 1 regulatory subunit 71 / PPP1R71 / Protein-tyrosine kinase 2 / p125FAK / pp125FAK


Mass: 18277.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q05397, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2500 mM Sodium chloride 100 mM Imidazole/ Hydrochloric acid pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.09→47.16 Å / Num. obs: 9713 / % possible obs: 99.5 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.165 / Net I/σ(I): 9.7
Reflection shellResolution: 2.09→2.15 Å / Rmerge(I) obs: 4.81 / Num. unique obs: 743 / CC1/2: 0.528 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVersion Jan 31, 2020data reduction
Aimless0.7.4data scaling
MoRDa1.4.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ow6

1ow6


Resolution: 2.093→47.155 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.661 / SU ML: 0.227 / Cross valid method: FREE R-VALUE / ESU R: 0.255 / ESU R Free: 0.216 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2862 485 5.004 %
Rwork0.2395 9208 -
all0.242 --
obs-9693 99.538 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.82 Å2
Baniso -1Baniso -2Baniso -3
1-5.137 Å20 Å2-0 Å2
2---5.653 Å20 Å2
3---0.516 Å2
Refinement stepCycle: LAST / Resolution: 2.093→47.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1126 0 0 13 1139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121154
X-RAY DIFFRACTIONr_angle_refined_deg1.541.6421567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2824.5151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92215222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.171155
X-RAY DIFFRACTIONr_chiral_restr0.1150.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02837
X-RAY DIFFRACTIONr_nbd_refined0.2220.2538
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2817
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.226
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3230.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2450.211
X-RAY DIFFRACTIONr_mcbond_it4.7756.07584
X-RAY DIFFRACTIONr_mcangle_it6.669.058730
X-RAY DIFFRACTIONr_scbond_it6.7476.62570
X-RAY DIFFRACTIONr_scangle_it9.5339.684837
X-RAY DIFFRACTIONr_lrange_it11.286114.6264666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.093-2.1470.448330.4136340.4157080.4520.42694.2090.387
2.147-2.2060.42350.3786530.3816880.4950.5551000.355
2.206-2.270.329330.3266290.3266630.7120.799.84920.296
2.27-2.340.399320.3126210.3166530.6740.7631000.282
2.34-2.4160.327320.2876030.2896350.6930.7971000.264
2.416-2.5010.218300.2825710.2796010.820.811000.249
2.501-2.5950.339300.285660.2835960.8010.8331000.255
2.595-2.70.379290.2785470.2835770.7780.85399.82670.248
2.7-2.820.352270.2855180.2895460.8290.85399.81680.253
2.82-2.9570.392260.2934920.2985180.8270.8711000.263
2.957-3.1160.287250.2834720.2834970.890.8771000.256
3.116-3.3050.333240.2514600.2544840.8590.8961000.234
3.305-3.5310.308220.2184220.2224450.8970.92599.77530.216
3.531-3.8130.316210.213990.2154200.8790.951000.22
3.813-4.1740.232200.1993730.2013930.9510.9671000.205
4.174-4.6620.288180.1923400.1973580.9620.9671000.2
4.662-5.3740.189160.1893010.1893170.9490.9561000.214
5.374-6.5610.3140.2442650.2472790.9150.9161000.267
6.561-9.190.231100.232070.2312170.9730.9691000.276
9.19-47.1550.17880.2421350.2391430.9920.9731000.295

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