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- PDB-7w7z: Crystal Structure of human Focal Adhesion Targeting (FAT) domain ... -

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Basic information

Entry
Database: PDB / ID: 7w7z
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: 2.15 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: Afaque, A.M. / Sandholu, A.S.
History
DepositionDec 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: 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
Water41423
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 area10910 Å2
Unit cell
Length a, b, c (Å)39.198, 94.429, 85.287
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

21A-1112-

HOH

31A-1114-

HOH

41A-1122-

HOH

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Components

#1: Protein Isoform 5 of Focal adhesion kinase 1


Mass: 18277.059 Da / Num. of mol.: 1 / Fragment: Focal adhesion targeting domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2, FAK, FAK1 / 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.: 23 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.0 M Lithium sulfate 0.1 M MES pH 6.5

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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: 2.15→42.64 Å / Num. obs: 8911 / % possible obs: 99.3 % / Redundancy: 13 % / Biso Wilson estimate: 55.62 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.071 / Χ2: 1.01 / Net I/σ(I): 17.1
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.68 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 680 / CC1/2: 0.62 / % possible all: 95

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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: 2.15→42.64 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.761 / SU ML: 0.184 / Cross valid method: FREE R-VALUE / ESU R: 0.235 / ESU R Free: 0.194
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2392 445 5.007 %
Rwork0.1952 8442 -
all0.197 --
obs-8887 99.23 %
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: 69.639 Å2
Baniso -1Baniso -2Baniso -3
1-0.053 Å20 Å20 Å2
2---0.064 Å20 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 2.15→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 0 23 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121149
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.6441560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68924.70651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33915223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.958155
X-RAY DIFFRACTIONr_chiral_restr0.1120.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02831
X-RAY DIFFRACTIONr_nbd_refined0.2260.2552
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2802
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2670.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2370.212
X-RAY DIFFRACTIONr_mcbond_it5.4166.469581
X-RAY DIFFRACTIONr_mcangle_it7.0139.657725
X-RAY DIFFRACTIONr_scbond_it8.6297.289567
X-RAY DIFFRACTIONr_scangle_it11.82310.563834
X-RAY DIFFRACTIONr_lrange_it13.517124.0054772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.455310.388583X-RAY DIFFRACTION96.3893
2.206-2.2660.293320.348601X-RAY DIFFRACTION99.061
2.266-2.3310.308300.293578X-RAY DIFFRACTION99.3464
2.331-2.4030.254290.252558X-RAY DIFFRACTION99.1554
2.403-2.4820.299290.269549X-RAY DIFFRACTION99.1424
2.482-2.5680.317280.244527X-RAY DIFFRACTION99.2844
2.568-2.6650.324280.238519X-RAY DIFFRACTION99.4545
2.665-2.7730.353260.24501X-RAY DIFFRACTION99.6219
2.773-2.8960.377240.247466X-RAY DIFFRACTION99.5935
2.896-3.0370.295250.205468X-RAY DIFFRACTION99.596
3.037-3.20.208230.206434X-RAY DIFFRACTION99.5643
3.2-3.3930.261220.209413X-RAY DIFFRACTION99.5423
3.393-3.6260.23200.19396X-RAY DIFFRACTION99.7602
3.626-3.9140.242200.175366X-RAY DIFFRACTION99.4845
3.914-4.2840.256170.17336X-RAY DIFFRACTION99.7175
4.284-4.7830.223160.153309X-RAY DIFFRACTION99.6933
4.783-5.5120.168150.169281X-RAY DIFFRACTION100
5.512-6.7220.354130.219241X-RAY DIFFRACTION100
6.722-9.3910.12100.145193X-RAY DIFFRACTION100
9.391-42.640.17670.163122X-RAY DIFFRACTION99.2308

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