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- PDB-1ow7: Paxillin LD4 motif bound to the Focal Adhesion Targeting (FAT) do... -

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Basic information

Entry
Database: PDB / ID: 1ow7
TitlePaxillin LD4 motif bound to the Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase
Components
  • Focal adhesion kinase 1
  • Paxillin
KeywordsTRANSFERASE / 4 helical bundle / amphiphatic helix
Function / homology
Function and homology information


netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of endothelial cell migration / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / regulation of epithelial cell migration / detection of muscle stretch / neuropilin binding / vinculin binding ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of endothelial cell migration / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / regulation of epithelial cell migration / detection of muscle stretch / neuropilin binding / vinculin binding / JUN kinase binding / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of macrophage proliferation / DCC mediated attractive signaling / Signal regulatory protein family interactions / positive regulation of fibroblast migration / regulation of GTPase activity / microtubule associated complex / MET activates PTK2 signaling / growth hormone receptor signaling pathway / regulation of focal adhesion assembly / negative regulation of cell-cell adhesion / regulation of osteoblast differentiation / positive regulation of wound healing / p130Cas linkage to MAPK signaling for integrins / Apoptotic cleavage of cellular proteins / positive regulation of macrophage chemotaxis / regulation of cytoskeleton organization / regulation of cell adhesion mediated by integrin / establishment of cell polarity / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of protein phosphorylation / vascular endothelial cell response to oscillatory fluid shear stress / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of protein kinase activity / negative regulation of anoikis / positive regulation of epithelial cell migration / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Smooth Muscle Contraction / RHO GTPases Activate WASPs and WAVEs / GAB1 signalosome / ephrin receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / endothelial cell migration / positive regulation of epithelial to mesenchymal transition / regulation of cell adhesion / heart morphogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / stress fiber / positive regulation of stress fiber assembly / Integrin signaling / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / SH2 domain binding / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / protein tyrosine phosphatase activity / axon guidance / peptidyl-tyrosine phosphorylation / molecular function activator activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / placenta development / integrin-mediated signaling pathway / cellular response to reactive oxygen species / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / cell motility / beta-catenin binding / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / integrin binding / epidermal growth factor receptor signaling pathway / positive regulation of protein phosphorylation / cell-cell junction / cell migration / regulation of cell shape / lamellipodium / regulation of cell population proliferation / protein autophosphorylation / actin binding / RAF/MAP kinase cascade / protein tyrosine kinase activity / angiogenesis / cell cortex / protein phosphatase binding / cytoskeleton / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / cilium / positive regulation of cell migration / ciliary basal body / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / centrosome / protein kinase binding / negative regulation of apoptotic process
Similarity search - Function
Paxillin / : / : / Paxillin family / Single helix bin / 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 ...Paxillin / : / : / Paxillin family / Single helix bin / 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 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Paxillin / Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHoellerer, M.K. / Noble, M.E.M. / Labesse, G. / Werner, J.M. / Arold, S.T.
CitationJournal: Structure / Year: 2003
Title: Molecular Recognition of Paxillin LD Motifs by the Focal Adhesion Targeting Domain
Authors: Hoellerer, M.K. / Noble, M.E.M. / Labesse, G. / Werner, J.M. / Arold, S.T.
History
DepositionMar 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Focal adhesion kinase 1
B: Focal adhesion kinase 1
C: Focal adhesion kinase 1
D: Paxillin
E: Paxillin
F: Paxillin


Theoretical massNumber of molelcules
Total (without water)57,8196
Polymers57,8196
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.994, 219.665, 96.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-60-

HOH

21C-4-

HOH

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Components

#1: Protein Focal adhesion kinase 1 / FADK 1 / pp125FAK / Protein- tyrosine kinase 2


Mass: 17836.539 Da / Num. of mol.: 3 / Fragment: Focal Adhesion Targeting Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2 OR FAK1 OR FAK / Plasmid: pGEX-6P2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05397, EC: 2.7.1.112
#2: Protein/peptide Paxillin


Mass: 1436.609 Da / Num. of mol.: 3 / Fragment: Paxillin LD4 motif / Source method: obtained synthetically / Details: Sequence derived from human paxillin / References: UniProt: P49023*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 4.77 Å3/Da / Density % sol: 74.01 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: sodium chloride, glycerol, Hepes, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13.9 M1reservoirNaCl
25 %glycerol1reservoir
3100 mMHEPES1reservoirpH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2002
Details: two crystals monochromator between two cylindrical parabolic mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→29.6 Å / Num. all: 23071 / Num. obs: 23071 / % possible obs: 88.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.064 / Net I/σ(I): 8.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 0.3 / Num. unique all: 1210 / Rsym value: 0.62 / % possible all: 79.3
Reflection
*PLUS
Num. measured all: 62275 / Rmerge(I) obs: 0.329
Reflection shell
*PLUS
% possible obs: 42.8 % / Rmerge(I) obs: 0.627

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbentry 1K05

1k05


Resolution: 2.6→111.8 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.46 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1) The second LD4 motif (chain F, bound to molecule C) was fitted into the unbiased 3Fo-2Fc maps (CNS). Its position and orientation were inferred from homology with the well-defined other ...Details: 1) The second LD4 motif (chain F, bound to molecule C) was fitted into the unbiased 3Fo-2Fc maps (CNS). Its position and orientation were inferred from homology with the well-defined other LD4 - FAT interaction (chains A and C), and are supported by NMR data(see publication). 2) The crystal diffracted anisotropically to 2.8 and 2.6 A resolution. The weak, but consistent, data to 2.6 A were included, as they significantly improved the electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.26947 1189 5.2 %RANDOM
Rwork0.23705 ---
all0.2387 23071 --
obs0.23871 23071 78.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 74.702 Å2
Baniso -1Baniso -2Baniso -3
1-7.65 Å20 Å20 Å2
2---3.19 Å20 Å2
3----4.46 Å2
Refinement stepCycle: LAST / Resolution: 2.6→111.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 0 50 3520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223509
X-RAY DIFFRACTIONr_bond_other_d00.023367
X-RAY DIFFRACTIONr_angle_refined_deg1.7132.014744
X-RAY DIFFRACTIONr_angle_other_deg3.4837895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.435442
X-RAY DIFFRACTIONr_chiral_restr0.1120.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023761
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02538
X-RAY DIFFRACTIONr_nbd_refined0.2510.21038
X-RAY DIFFRACTIONr_nbd_other0.2940.23922
X-RAY DIFFRACTIONr_nbtor_other0.1070.21835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.25
X-RAY DIFFRACTIONr_mcbond_it2.8281.52252
X-RAY DIFFRACTIONr_mcangle_it5.03723644
X-RAY DIFFRACTIONr_scbond_it4.74331257
X-RAY DIFFRACTIONr_scangle_it7.5984.51100
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.463 48
Rwork0.435 785
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 29.6 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.71

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