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- PDB-2aeh: Focal adhesion kinase 1 -

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Basic information

Entry
Database: PDB / ID: 2aeh
TitleFocal adhesion kinase 1
ComponentsFocal adhesion kinase 1PTK2
KeywordsTRANSFERASE / FERM domain
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / angiogenesis involved in wound healing / signal complex assembly / response to pH / negative regulation of cell-substrate adhesion / wound healing, spreading of cells / positive regulation of focal adhesion assembly / negative regulation of anoikis / positive regulation of protein tyrosine kinase activity / regulation of cell adhesion / response to muscle stretch / ciliary basal body / molecular function activator activity / actin filament organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / sarcolemma / integrin binding / positive regulation of protein binding / cell cortex / protein tyrosine kinase activity / angiogenesis / protease binding / dendritic spine / protein autophosphorylation / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Acyl-CoA Binding Protein - #10 / 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 / Acyl-CoA Binding Protein ...Acyl-CoA Binding Protein - #10 / 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 / Acyl-CoA Binding Protein / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / 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 / Roll / Roll / 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Focal adhesion kinase 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.53 Å
AuthorsCeccarelli, D.F. / Song, H.K. / Poy, F. / Schaller, M.D. / Eck, M.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of the FERM Domain of Focal Adhesion Kinase
Authors: Ceccarelli, D.F. / Song, H.K. / Poy, F. / Schaller, M.D. / Eck, M.J.
History
DepositionJul 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: Focal adhesion kinase 1
B: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)84,6002
Polymers84,6002
Non-polymers00
Water4,378243
1
A: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)42,3001
Polymers42,3001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)42,3001
Polymers42,3001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.213, 146.231, 68.919
Angle α, β, γ (deg.)90.00, 96.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Focal adhesion kinase 1 / PTK2 / FADK 1 / PP125FAK


Mass: 42300.109 Da / Num. of mol.: 2 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: FAK1, FAK / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q00944, EC: 2.7.1.112
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris pH 8.0, 16-22% PEG 4000, 20% glycerol, 200 mM NaCl, 100 mM CsCl, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F210.9796,0.9793,0.95004
SYNCHROTRONNSLS X12B20.97897
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDMay 3, 2002
CUSTOM-MADE2CCDMay 3, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1channel-cut crystalMADMx-ray1
2channel-cut crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97931
30.950041
40.978971
ReflectionResolution: 2.5→28.6 Å / Num. all: 29870 / Num. obs: 29870 / % possible obs: 100 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 4.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 22.5
Reflection shellResolution: 2.53→2.57 Å / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.53→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1405 -RANDOM
Rwork0.206 ---
all0.21 29992 --
obs0.21 28442 94.8 %-
Refinement stepCycle: LAST / Resolution: 2.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5369 0 0 243 5612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID
2.5-2.530.379420.315X-RAY DIFFRACTION
7.46-200.168520.152X-RAY DIFFRACTION

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