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- PDB-1ow6: Paxillin LD4 motif bound to the Focal Adhesion Targeting (FAT) do... -

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Basic information

Entry
Database: PDB / ID: 1ow6
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 / domain swapping / 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 / establishment of cell polarity / regulation of cytoskeleton organization / regulation of cell adhesion mediated by integrin / 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 / Smooth Muscle Contraction / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / GAB1 signalosome / vascular endothelial growth factor receptor signaling pathway / ephrin 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 / placenta development / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / 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 / actin binding / protein autophosphorylation / RAF/MAP kinase cascade / protein tyrosine kinase activity / cell cortex / angiogenesis / protein phosphatase binding / cytoskeleton / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / cilium / ciliary basal body / positive regulation of cell migration / 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: 2.35 Å
AuthorsHoellerer, M.K. / Noble, M.E.M. / Labesse, G. / Campbell, I.D. / Werner, J.M. / Arold, S.T.
Citation
Journal: 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. / Campbell, I.D. / Werner, J.M. / Arold, S.T.
#1: Journal: Structure / Year: 2002
Title: The Structural Basis of Localization and Signaling by the Focal Adhesion Targeting Domain
Authors: Arold, S.T. / Hoellerer, M. / Noble, M.E.M.
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 1.3Jan 22, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_biol
Revision 1.4Aug 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
F: Paxillin


Theoretical massNumber of molelcules
Total (without water)56,3835
Polymers56,3835
Non-polymers00
Water2,144119
1
A: Focal adhesion kinase 1
D: Paxillin

A: Focal adhesion kinase 1
D: Paxillin


Theoretical massNumber of molelcules
Total (without water)38,5464
Polymers38,5464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6260 Å2
ΔGint-65 kcal/mol
Surface area16460 Å2
MethodPISA
2
B: Focal adhesion kinase 1

B: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)35,6732
Polymers35,6732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1520 Å2
ΔGint-14 kcal/mol
Surface area14570 Å2
MethodPISA
3
C: Focal adhesion kinase 1
F: Paxillin

C: Focal adhesion kinase 1
F: Paxillin


Theoretical massNumber of molelcules
Total (without water)38,5464
Polymers38,5464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3200 Å2
ΔGint-28 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.308, 223.274, 96.992
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
11A-73-

HOH

21B-60-

HOH

31C-4-

HOH

41C-90-

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.: 2 / 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.: 119 / 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: 4.9 Å3/Da / Density % sol: 74.68 %
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: BM14 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→41.6 Å / Num. all: 39088 / Num. obs: 39088 / % possible obs: 97.3 % / Redundancy: 3 % / Biso Wilson estimate: 50.49 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.081 / Net I/σ(I): 7.2
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 1 / Num. unique all: 5762 / Rsym value: 0.749 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 116554 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.75

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Processing

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

1k05


Resolution: 2.35→37.27 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 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 - ...Details: 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).
RfactorNum. reflection% reflectionSelection details
Rfree0.27357 1980 5.1 %RANDOM
Rwork0.24161 ---
all0.2432 39088 --
obs0.24326 39088 96.85 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.524 Å2
Baniso -1Baniso -2Baniso -3
1-7.69 Å20 Å20 Å2
2---5.3 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.35→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 0 119 3488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223410
X-RAY DIFFRACTIONr_bond_other_d0.0080.023274
X-RAY DIFFRACTIONr_angle_refined_deg2.2112.0094613
X-RAY DIFFRACTIONr_angle_other_deg1.00637678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3095430
X-RAY DIFFRACTIONr_chiral_restr0.1130.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023656
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02522
X-RAY DIFFRACTIONr_nbd_refined0.2430.21011
X-RAY DIFFRACTIONr_nbd_other0.2490.23934
X-RAY DIFFRACTIONr_nbtor_other0.0980.22009
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.2122
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.218
X-RAY DIFFRACTIONr_mcbond_it1.7211.52187
X-RAY DIFFRACTIONr_mcangle_it3.15723542
X-RAY DIFFRACTIONr_scbond_it3.95731223
X-RAY DIFFRACTIONr_scangle_it6.6414.51071
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.428 155
Rwork0.436 2747
Refinement
*PLUS
Lowest resolution: 41.6 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.242
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_deg2.21

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