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- PDB-1k40: crystal structure of the FAT domain of focal adhesion kinase -

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Basic information

Entry
Database: PDB / ID: 1k40
Titlecrystal structure of the FAT domain of focal adhesion kinase
Componentsadhesion kinase
KeywordsTRANSFERASE / HELIX BUNDLE
Function / homology
Function and homology information


DCC mediated attractive signaling / Apoptotic cleavage of cellular proteins / MET activates PTK2 signaling / NCAM signaling for neurite out-growth / negative regulation of synapse assembly / RHO GTPases Activate WASPs and WAVEs / regulation of substrate adhesion-dependent cell spreading / central nervous system neuron axonogenesis / EPHB-mediated forward signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins ...DCC mediated attractive signaling / Apoptotic cleavage of cellular proteins / MET activates PTK2 signaling / NCAM signaling for neurite out-growth / negative regulation of synapse assembly / RHO GTPases Activate WASPs and WAVEs / regulation of substrate adhesion-dependent cell spreading / central nervous system neuron axonogenesis / EPHB-mediated forward signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / negative regulation of organ growth / Extra-nuclear estrogen signaling / negative regulation of axonogenesis / regulation of epithelial cell migration / RAF/MAP kinase cascade / intracellular chloride ion homeostasis / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell-cell adhesion mediated by integrin / regulation of modification of postsynaptic actin cytoskeleton / JUN kinase binding / VEGFA-VEGFR2 Pathway / signal complex assembly / negative regulation of cell adhesion mediated by integrin / regulation of cell adhesion mediated by integrin / positive regulation of macrophage proliferation / peptidyl-tyrosine autophosphorylation / negative regulation of cell-cell adhesion / positive regulation of fibroblast migration / growth hormone receptor signaling pathway / positive regulation of ubiquitin-dependent protein catabolic process / regulation of focal adhesion assembly / positive regulation of smooth muscle cell migration / nuclear migration / positive regulation of wound healing / positive regulation of cardiac muscle hypertrophy / regulation of osteoblast differentiation / blood vessel development / positive regulation of macrophage chemotaxis / positive regulation of epithelial cell migration / negative regulation of anoikis / intercalated disc / positive regulation of glial cell proliferation / ephrin receptor signaling pathway / vasculogenesis / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / endothelial cell migration / regulation of cell adhesion / positive regulation of synaptic transmission / phosphatase binding / phosphatidylinositol 3-kinase binding / JNK cascade / extracellular matrix organization / stress fiber / ciliary tip / peptidyl-tyrosine phosphorylation / transforming growth factor beta receptor signaling pathway / protein tyrosine phosphatase activity / positive regulation of smooth muscle cell proliferation / positive regulation of cell adhesion / positive regulation of phagocytosis / SH2 domain binding / molecular function activator activity / negative regulation of cell migration / integrin-mediated signaling pathway / negative regulation of autophagy / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / sarcolemma / microtubule cytoskeleton organization / integrin binding / neuron migration / vasodilation / epidermal growth factor receptor signaling pathway / MAPK cascade / protein autophosphorylation / regulation of cell population proliferation / regulation of cell shape / cell migration / lamellipodium / positive regulation of cell growth / actin binding / protein tyrosine kinase activity / angiogenesis / protein phosphatase binding / cell cortex / basolateral plasma membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cilium / postsynapse / apical plasma membrane / ciliary basal body / nuclear body / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsHayashi, I. / Vuori, K. / Liddington, R.C.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The focal adhesion targeting (FAT) region of focal adhesion kinase is a four-helix bundle that binds paxillin
Authors: Hayashi, I. / Vuori, K. / Liddington, R.C.
History
DepositionOct 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: adhesion kinase


Theoretical massNumber of molelcules
Total (without water)14,0061
Polymers14,0061
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.104, 40.163, 52.008
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein adhesion kinase


Mass: 14006.386 Da / Num. of mol.: 1 / Fragment: FAT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P34152, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: PEG10k, HEPES, pH 7.0, VAPOR DIFFUSION, temperature 295K
Crystal grow
*PLUS
Method: batch method / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
120 mMTris-HCl1droppH8.0
20.1 M1dropNaCl
31 mMdithiothreitol1drop
425 mg/mlprotein1drop
50.1 MHEPES1reservoirpH7.0
620 %(w/v)PEG100001reservoir

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 8, 2001
RadiationMonochromator: Channel Cut Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionNum. all: 5618 / Num. obs: 5964 / Observed criterion σ(F): 1 / Biso Wilson estimate: 17.7 Å2
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 20 Å / % possible obs: 98.2 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 91.9 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 6.05

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
CNS1refinement
DMphasing
RefinementResolution: 2.25→18.66 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1112998.34 / Data cutoff high rms absF: 1112998.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 318 5.7 %RANDOM
Rwork0.236 ---
obs0.236 5618 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6602 Å2 / ksol: 0.399858 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.8 Å20 Å2-7.44 Å2
2--5.07 Å20 Å2
3---0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.25→18.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 0 24 1001
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d1.79
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 53 5.9 %
Rwork0.242 850 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 5300 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.224 / Rfactor Rfree: 0.275
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.79
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.356 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.242

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