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- PDB-3gm3: Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 -

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Basic information

Entry
Database: PDB / ID: 3gm3
TitleCrystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2
ComponentsProtein tyrosine kinase 2 beta
KeywordsTRANSFERASE / four-helix bundle
Function / homology
Function and homology information


regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / negative regulation of bone mineralization / cortical cytoskeleton organization / regulation of postsynaptic density assembly ...regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / negative regulation of bone mineralization / cortical cytoskeleton organization / regulation of postsynaptic density assembly / activation of Janus kinase activity / chemokine-mediated signaling pathway / apical dendrite / cellular response to fluid shear stress / regulation of release of sequestered calcium ion into cytosol / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / calcium/calmodulin-dependent protein kinase activity / sprouting angiogenesis / Interleukin-2 signaling / Signal regulatory protein family interactions / NMDA selective glutamate receptor complex / positive regulation of cell-matrix adhesion / positive regulation of actin filament polymerization / Golgi organization / negative regulation of potassium ion transport / positive regulation of protein kinase activity / RHOU GTPase cycle / signaling receptor activator activity / peptidyl-tyrosine autophosphorylation / positive regulation of excitatory postsynaptic potential / vascular endothelial growth factor receptor signaling pathway / bone resorption / postsynaptic density, intracellular component / cellular defense response / regulation of cell adhesion / tumor necrosis factor-mediated signaling pathway / cellular response to retinoic acid / ionotropic glutamate receptor binding / positive regulation of endothelial cell migration / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of neuron projection development / regulation of synaptic plasticity / VEGFA-VEGFR2 Pathway / long-term synaptic potentiation / epidermal growth factor receptor signaling pathway / neuron migration / positive regulation of angiogenesis / lamellipodium / regulation of cell shape / presynapse / cell body / protein autophosphorylation / protein-containing complex assembly / growth cone / protein tyrosine kinase activity / cell cortex / adaptive immune response / negative regulation of neuron apoptotic process / cytoskeleton / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynaptic density / protein phosphorylation / positive regulation of cell migration / negative regulation of cell population proliferation / focal adhesion / neuronal cell body / apoptotic process / positive regulation of cell population proliferation / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 central domain ...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 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) / 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
Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLulo, J.E. / Yuzawa, S. / Schlessinger, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structures of free and ligand-bound focal adhesion targeting domain of Pyk2
Authors: Lulo, J. / Yuzawa, S. / Schlessinger, J.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Protein tyrosine kinase 2 beta


Theoretical massNumber of molelcules
Total (without water)16,6921
Polymers16,6921
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.462, 42.791, 129.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Protein tyrosine kinase 2 beta


Mass: 16692.205 Da / Num. of mol.: 1
Fragment: Focal Adhesion Targeting (FAT) Domain, UNP residues 861-1009
Mutation: C899A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14289, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 8000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2006
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 5467 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.4.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GM2

3gm2


Resolution: 2.6→32.38 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.447 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.704 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28871 232 4.5 %RANDOM
Rwork0.25467 ---
obs0.25625 5186 98.12 %-
all-5467 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.947 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--1.23 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.6→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 0 14 1011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221003
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2162.0091365
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45726.15439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.57715184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.608156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021716
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_it0.911.5664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34521067
X-RAY DIFFRACTIONr_scbond_it1.3793339
X-RAY DIFFRACTIONr_scangle_it2.5124.5298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 17 -
Rwork0.297 294 -
obs--84.51 %

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