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- PDB-2j0k: Crystal structure of a fragment of focal adhesion kinase containi... -

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Basic information

Entry
Database: PDB / ID: 2j0k
TitleCrystal structure of a fragment of focal adhesion kinase containing the FERM and kinase domains.
ComponentsFOCAL ADHESION KINASE 1
KeywordsTRANSFERASE / CELL MIGRATION / INTEGRIN SIGNALING
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / negative regulation of protein autophosphorylation / radial glia-guided pyramidal neuron migration / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / negative regulation of protein autophosphorylation / radial glia-guided pyramidal neuron migration / 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 / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / signal complex assembly / response to pH / angiogenesis involved in wound healing / wound healing, spreading of cells / positive regulation of protein tyrosine kinase activity / negative regulation of anoikis / negative regulation of cell-substrate adhesion / positive regulation of focal adhesion assembly / positive regulation of protein binding / regulation of cell adhesion / response to muscle stretch / molecular function activator activity / actin filament organization / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / sarcolemma / integrin binding / epidermal growth factor receptor signaling pathway / protein autophosphorylation / protease binding / protein tyrosine kinase activity / cell cortex / positive regulation of cell migration / ciliary basal body / focal adhesion / positive regulation of cell population proliferation / centrosome / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Ubiquitin-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,2,3,4-TETRAHYDROGEN-STAUROSPORINE / Focal adhesion kinase 1
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLietha, D. / Cai, X. / Li, Y. / Schaller, M.D. / Eck, M.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structural Basis for the Autoinhibition of Focal Adhesion Kinase.
Authors: Lietha, D. / Cai, X. / Li, Y. / Schaller, M.D. / Eck, M.J.
History
DepositionAug 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,5864
Polymers150,6452
Non-polymers9412
Water90150
1
A: FOCAL ADHESION KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7932
Polymers75,3221
Non-polymers4711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FOCAL ADHESION KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7932
Polymers75,3221
Non-polymers4711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.022, 106.209, 240.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.0017, 0.0073), (0.0029, 0.9867, 0.1627), (-0.007, 0.1627, -0.9866)
Vector: 28.602, -11.8664, 126.2394)

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Components

#1: Protein FOCAL ADHESION KINASE 1 / FOCAL ADHESION KINASE / FADK 1 / PP125FAK


Mass: 75322.281 Da / Num. of mol.: 2 / Fragment: FERM AND KINASE DOMAIN, RESIDUES 31-686
Source method: isolated from a genetically manipulated source
Details: UNPHOSPHORYLATED / Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PACG2T / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: Q00944, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-4ST / 1,2,3,4-TETRAHYDROGEN-STAUROSPORINE / AFN941


Mass: 470.563 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H30N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 31-686

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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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growpH: 8.5
Details: 15% PEG10K, 300MM NACL, 100MM TRIS PH8.5, 10MM TCEP, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 32779 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.57
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.13 / % possible all: 70.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1MP8 AND 2AEH

1mp8

2aeh


Resolution: 3→38.49 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.886 / SU B: 27.34 / SU ML: 0.431 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.522 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1636 5.1 %RANDOM
Rwork0.234 ---
obs0.237 30750 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 3→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9782 0 70 50 9902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.97413594
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91651202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4823.755474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.274151788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2641576
X-RAY DIFFRACTIONr_chiral_restr0.0910.21491
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027562
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.24571
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.26826
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2306
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0470.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.551.56189
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97429770
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.89434552
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5844.53824
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 92 -
Rwork0.314 1636 -
obs--72.79 %
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)
18.48261.81654.67755.91710.41057.2874-0.11950.25580.5182-0.29620.2235-0.5596-0.54150.7472-0.104-0.28380.06570.10030.0215-0.0938-0.183112.64518.50544.999
24.5315-2.453-1.85610.22912.03122.6976-0.3349-0.1153-0.8725-0.02-0.17650.36120.5952-0.28960.5114-0.11360.0156-0.0005-0.0263-0.0085-0.03741.575-4.84638.237
33.3818-0.5476-9.76358.18277.118134.69730.1853-0.1829-1.3085-0.2373-0.265-0.5042-0.1294-1.150.0797-0.19020.0993-0.1473-0.02210.0571-0.2068-7.32314.57957.137
43.4369-2.2768-0.605713.80681.41619.34760.16690.99110.4621-0.8503-0.38330.546-1.2925-0.44140.21640.01830.1136-0.04790.00880.0583-0.2689-11.4460.389107.599
57.6051-3.3525-2.435.9771.49564.6941-0.35180.015-0.16890.7058-0.0410.51510.5341-0.12410.39280.1039-0.02760.0167-0.4683-0.0612-0.52081.163-23.675109.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 127
2X-RAY DIFFRACTION2A128 - 253
3X-RAY DIFFRACTION3A254 - 263
4X-RAY DIFFRACTION4B414 - 503
5X-RAY DIFFRACTION5B504 - 686

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