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- PDB-1k04: Crystal Structure of the Focal Adhesion Targeting Domain of Focal... -

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Basic information

Entry
Database: PDB / ID: 1k04
TitleCrystal Structure of the Focal Adhesion Targeting Domain of Focal Adhesion Kinase
ComponentsFOCAL ADHESION KINASE 1
KeywordsTRANSFERASE / up-down-up-down four helical bundle forming a helix-exchange dimer
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
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 / 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. / 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 / 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: 1.95 Å
AuthorsArold, S.T. / Hoellerer, M.K. / Noble, M.E.M.
CitationJournal: Structure / Year: 2002
Title: The structural basis of localization and signaling by the focal adhesion targeting domain.
Authors: Arold, S.T. / Hoellerer, M.K. / Noble, M.E.
History
DepositionSep 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9852
Polymers17,9501
Non-polymers351
Water1,74797
1
A: FOCAL ADHESION KINASE 1
hetero molecules

A: FOCAL ADHESION KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9704
Polymers35,8992
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4710 Å2
ΔGint-52 kcal/mol
Surface area16940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)38.426, 95.555, 84.821
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-200-

CL

21A-1-

HOH

31A-52-

HOH

41A-107-

HOH

DetailsThe second protomer of the dimeric assembly is generated by the two fold axis: -X,-Y,1/2+Z

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Components

#1: Protein FOCAL ADHESION KINASE 1 / FADK 1


Mass: 17949.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAK / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q05397, EC: 2.7.1.112
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.17 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, NaCl, Na/K phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-HCl1droppH8.0
2150 mM1dropNaCl
32 mMEDTA1drop
42 mMdithiothreitol1drop
520 mg/mlprotein1drop
60.1 MMES1reservoirpH6.5
72.0 M1reservoirNaCl
80.2 Msodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.95→47.7 Å / Num. obs: 11110 / % possible obs: 94.8 % / Observed criterion σ(F): 0.9 / Observed criterion σ(I): 0.9 / Redundancy: 3.3 % / Biso Wilson estimate: 45.7 Å2 / Rsym value: 0.056 / Net I/σ(I): 2.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 2462 / Rsym value: 0.509 / % possible all: 88.9
Reflection
*PLUS
Num. measured all: 36960 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 88.9 % / Rmerge(I) obs: 0.509

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.7 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 719 7.2 %random
Rwork0.243 ---
all-11110 --
obs-11110 94.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--19.527 Å20 Å20 Å2
2--12.764 Å20 Å2
3---6.763 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 1 97 1196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.001
X-RAY DIFFRACTIONp_angle_d1.4
LS refinement shellResolution: 1.95→2.02 Å
RfactorNum. reflection% reflection
Rfree0.43 51 -
Rwork0.44 --
obs-999 8.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
Refinement
*PLUS
% reflection Rfree: 7 % / Rfactor obs: 0.243 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.43 / Rfactor Rwork: 0.44

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