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- PDB-3s9o: The Focal Adhesion Targeting (FAT) domain of the Focal Adhesion K... -

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Basic information

Entry
Database: PDB / ID: 3s9o
TitleThe Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase showing N-terminal interactions in cis
ComponentsFocal adhesion kinase 1PTK2
KeywordsTRANSFERASE / 4-helix bundle / focal adhesion targeting / protein binding / phosphorylation / nucleus
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 macrophage proliferation / positive regulation of fibroblast migration ...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 macrophage proliferation / positive regulation of fibroblast migration / DCC mediated attractive signaling / Signal regulatory protein family interactions / growth hormone receptor signaling pathway / regulation of osteoblast differentiation / regulation of cytoskeleton organization / MET activates PTK2 signaling / regulation of focal adhesion assembly / establishment of cell polarity / positive regulation of wound healing / positive regulation of macrophage chemotaxis / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / negative regulation of cell-cell adhesion / Apoptotic cleavage of cellular proteins / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / positive regulation of epithelial to mesenchymal transition / ephrin receptor signaling pathway / positive regulation of protein kinase activity / vascular endothelial growth factor receptor signaling pathway / regulation of cell adhesion / heart morphogenesis / stress fiber / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / SH2 domain binding / Integrin signaling / transforming growth factor beta receptor signaling pathway / ciliary basal body / placenta development / protein tyrosine phosphatase activity / molecular function activator activity / cell motility / integrin-mediated signaling pathway / axon guidance / FCGR3A-mediated phagocytosis / regulation of protein phosphorylation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cell migration / integrin binding / actin binding / regulation of cell population proliferation / cell cortex / regulation of cell shape / RAF/MAP kinase cascade / protein phosphatase binding / angiogenesis / protein tyrosine kinase activity / dendritic spine / Extra-nuclear estrogen signaling / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / positive regulation of protein phosphorylation / focal adhesion / intracellular membrane-bounded organelle / 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
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 ...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 / 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) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsArold, S.T.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Conformational dynamics of the focal adhesion targeting domain control specific functions of focal adhesion kinase in cells.
Authors: Kadare, G. / Gervasi, N. / Brami-Cherrier, K. / Blockus, H. / El Messari, S. / Arold, S.T. / Girault, J.A.
History
DepositionJun 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Focal adhesion kinase 1
B: Focal adhesion kinase 1
C: Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3936
Polymers54,3123
Non-polymers813
Water59433
1
A: Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1623
Polymers18,1041
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)18,1041
Polymers18,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1272
Polymers18,1041
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.918, 223.983, 98.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Focal adhesion kinase 1 / PTK2 / FADK 1 / Protein-tyrosine kinase 2 / pp125FAK


Mass: 18103.863 Da / Num. of mol.: 3
Fragment: focal adhesion targeting domain (UNP Residue 891-1052)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAK, FAK1, PTK2 / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS
References: UniProt: Q05397, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4.54 Å3/Da / Density % sol: 72.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Hepes, 3.3M NaCl, 1% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.97984 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97984 Å / Relative weight: 1
ReflectionResolution: 2.6→30.43 Å / Num. all: 25973 / Num. obs: 25973 / % possible obs: 84.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.09 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.4 / Num. unique all: 2416 / Rsym value: 0.386 / % possible all: 54

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K05

1k05


Resolution: 2.6→30.43 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 22.572 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28721 546 2.1 %RANDOM
Rwork0.23294 ---
all0.23408 25973 --
obs0.23408 25427 84.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.285 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--0.23 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 3 33 3307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223315
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0082.0144496
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0575420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.97926.719128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.79415647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3961512
X-RAY DIFFRACTIONr_chiral_restr0.1240.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212380
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8471.52129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68823461
X-RAY DIFFRACTIONr_scbond_it2.9131186
X-RAY DIFFRACTIONr_scangle_it4.9754.51035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 23 -
Rwork0.303 1097 -
obs--49.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.02240.0864-2.83950.0073-0.247.88591.30781.53991.0775-0.4011-1.9082-0.58881.7793-0.34790.60050.930.2118-0.51620.3388-0.31680.929524.85535.41621.212
23.6568-1.24390.05982.3127-0.0392.09910.0014-0.09780.1749-0.066-0.0028-0.10750.02170.09040.00140.3188-0.0226-0.00930.2444-0.00560.203233.44831.53533.412
33.6523-4.10661.29535.9537-1.33851.9556-0.0299-0.2208-0.23530.11870.09610.50090.1256-0.1606-0.06610.3659-0.05910.00630.233-0.01050.264127.62623.62435.142
43.5067-2.4578-1.02716.23592.47295.4557-0.11060.0387-0.06760.24980.01230.11750.2258-0.06820.09830.2222-0.0272-0.04250.2861-0.00530.30281.2559.7531.131
54.4202-4.3329-3.98175.77913.78584.2996-0.0906-0.2198-0.24740.26140.0882-0.04030.13230.18310.00230.2942-0.0096-0.07820.2985-0.04010.21748.51263.08939.985
61.1848-1.6627-0.65625.21942.72792.69570.1074-0.0379-0.0441-0.0707-0.0211-0.1847-0.1406-0.0435-0.08630.30210.0048-0.00380.24420.00930.2197.02771.06736.278
74.4468-3.02770.49029.10320.39984.1016-0.07290.1159-0.04070.05390.1355-0.36110.0618-0.1166-0.06270.3889-0.00220.05220.20760.02430.09063.741103.21228.753
86.5277-3.2003-1.3784.0021.89770.9047-0.00950.2988-0.5304-0.6675-0.0082-0.97390.00250.7350.01760.4269-0.03470.08880.30010.03580.570221.79790.74330.199
92.3165-2.2435-0.0375.99720.00321.7182-0.1272-0.0485-0.12080.29280.1742-0.247-0.0296-0.1026-0.04710.3315-0.0348-0.00130.263-0.00710.20177.12393.40136.981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A909 - 918
2X-RAY DIFFRACTION2A919 - 978
3X-RAY DIFFRACTION3A979 - 1049
4X-RAY DIFFRACTION4B907 - 942
5X-RAY DIFFRACTION5B943 - 982
6X-RAY DIFFRACTION6B983 - 1047
7X-RAY DIFFRACTION7C908 - 937
8X-RAY DIFFRACTION8C938 - 962
9X-RAY DIFFRACTION9C963 - 1048

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