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- PDB-4ny0: Crystal structure of FERM domain of human focal adhesion kinase -

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Basic information

Entry
Database: PDB / ID: 4ny0
TitleCrystal structure of FERM domain of human focal adhesion kinase
ComponentsFocal adhesion kinase 1
KeywordsTRANSFERASE / FERM domain / focal adhesion kinase / focal targeting domain / integrin signaling
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 / JUN kinase binding / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of macrophage proliferation / DCC mediated attractive signaling ...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 / JUN kinase binding / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of macrophage proliferation / DCC mediated attractive signaling / positive regulation of fibroblast migration / Signal regulatory protein family interactions / regulation of GTPase activity / growth hormone receptor signaling pathway / MET activates PTK2 signaling / regulation of focal adhesion assembly / negative regulation of cell-cell adhesion / positive regulation of wound healing / p130Cas linkage to MAPK signaling for integrins / regulation of osteoblast differentiation / Apoptotic cleavage of cellular proteins / establishment of cell polarity / positive regulation of macrophage chemotaxis / regulation of cytoskeleton organization / regulation of cell adhesion mediated by integrin / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of protein phosphorylation / negative regulation of anoikis / positive regulation of epithelial cell migration / ephrin receptor signaling pathway / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / positive regulation of protein kinase activity / vascular endothelial growth factor receptor signaling pathway / regulation of cell adhesion / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / stress fiber / EPHB-mediated forward signaling / Integrin signaling / protein tyrosine phosphatase activity / NCAM signaling for neurite out-growth / transforming growth factor beta receptor signaling pathway / SH2 domain binding / axon guidance / molecular function activator activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / integrin-mediated signaling pathway / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / cell motility / placenta development / peptidyl-tyrosine phosphorylation / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / epidermal growth factor receptor signaling pathway / integrin binding / cell migration / regulation of cell shape / regulation of cell population proliferation / positive regulation of protein phosphorylation / actin binding / RAF/MAP kinase cascade / cell cortex / protein autophosphorylation / protein tyrosine kinase activity / protein phosphatase binding / angiogenesis / cytoskeleton / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ciliary basal body / cilium / positive regulation of cell migration / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / centrosome / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Acyl-CoA Binding Protein - #10 / 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 / Acyl-CoA Binding Protein ...Acyl-CoA Binding Protein - #10 / 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 / Acyl-CoA Binding Protein / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-domain like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / 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 / Roll / Roll / 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsWalkiewicz, K. / Arold, S.T.
CitationJournal: Embo J. / Year: 2014
Title: FAK dimerization controls its kinase-dependent functions at focal adhesions.
Authors: Brami-Cherrier, K. / Gervasi, N. / Arsenieva, D. / Walkiewicz, K. / Boutterin, M.C. / Ortega, A. / Leonard, P.G. / Seantier, B. / Gasmi, L. / Bouceba, T. / Kadare, G. / Girault, J.A. / Arold, S.T.
History
DepositionDec 10, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Focal adhesion kinase 1
A: Focal adhesion kinase 1
B: Focal adhesion kinase 1
C: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)172,5084
Polymers172,5084
Non-polymers00
Water00
1
D: Focal adhesion kinase 1
B: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)86,2542
Polymers86,2542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Focal adhesion kinase 1
C: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)86,2542
Polymers86,2542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.960, 152.500, 95.340
Angle α, β, γ (deg.)90.000, 93.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
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: 43127.078 Da / Num. of mol.: 4 / Fragment: FERM domain, UNP RESIDUES 31-405 / Mutation: F85L, W181G
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

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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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG 10000, 0.1M Ammonium Sulfate, 0.1M bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.8→95.15 Å / Num. obs: 49012 / Redundancy: 2 % / Biso Wilson estimate: 74.77 Å2 / Rmerge(I) obs: 0.047
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.8-2.9320.6511.44968179.5
2.93-3.0820.4252.26116197.1
3.08-3.2720.2223.863151100
3.27-3.5320.126.662851100
3.53-3.8820.06510.662831100
3.88-4.4420.0371663401100
4.44-5.620.02619.363271100
5.6-95.1520.01822.26378199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
MOLREPphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→95.15 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8187 / SU ML: 0.44 / σ(F): 1.35 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 2478 5.06 %RANDOM
Rwork0.1933 ---
obs0.1952 48993 97.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.26 Å2 / Biso mean: 76.8297 Å2 / Biso min: 32.85 Å2
Refinement stepCycle: LAST / Resolution: 2.8→95.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10722 0 0 0 10722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110953
X-RAY DIFFRACTIONf_angle_d1.40914785
X-RAY DIFFRACTIONf_chiral_restr0.061620
X-RAY DIFFRACTIONf_plane_restr0.0071897
X-RAY DIFFRACTIONf_dihedral_angle_d13.6984139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.85380.40031150.33511967208275
2.8538-2.91210.3319980.31752202230083
2.9121-2.97540.34281360.28282425256191
2.9754-3.04460.31971510.26492592274399
3.0446-3.12080.32051360.251126762812100
3.1208-3.20510.28051280.237726362764100
3.2051-3.29950.2921370.237726962833100
3.2995-3.4060.27211160.236526872803100
3.406-3.52770.29091450.218226392784100
3.5277-3.66890.26331350.203126682803100
3.6689-3.83590.24861390.194826722811100
3.8359-4.03820.22911650.18425992764100
4.0382-4.29120.21141520.172326852837100
4.2912-4.62250.18481620.159926372799100
4.6225-5.08760.21121340.15426762810100
5.0876-5.82370.23271280.177326952823100
5.8237-7.33690.19471480.226762824100
7.3369-95.20470.18041530.1642687284099

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