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- PDB-3gm2: Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 -

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Basic information

Entry
Database: PDB / ID: 3gm2
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 / response to cation stress / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / negative regulation of myeloid cell differentiation / blood vessel endothelial cell migration / endothelin receptor signaling pathway ...regulation of macrophage chemotaxis / response to cation stress / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / negative regulation of myeloid cell differentiation / blood vessel endothelial cell migration / endothelin receptor signaling pathway / regulation of postsynaptic density assembly / apical dendrite / negative regulation of muscle cell apoptotic process / negative regulation of bone mineralization / cortical cytoskeleton organization / activation of Janus kinase activity / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to fluid shear stress / regulation of release of sequestered calcium ion into cytosol / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity / Interleukin-2 signaling / long-term synaptic depression / sprouting angiogenesis / NMDA selective glutamate receptor complex / oocyte maturation / Signal regulatory protein family interactions / positive regulation of cell-matrix adhesion / positive regulation of actin filament polymerization / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / stress fiber assembly / negative regulation of potassium ion transport / RHOU GTPase cycle / positive regulation of excitatory postsynaptic potential / response to immobilization stress / postsynaptic density, intracellular component / positive regulation of protein kinase activity / glutamate receptor binding / glial cell proliferation / cellular defense response / regulation of cell adhesion / bone resorption / vascular endothelial growth factor receptor signaling pathway / response to glucose / response to mechanical stimulus / peptidyl-tyrosine autophosphorylation / cellular response to retinoic acid / tumor necrosis factor-mediated signaling pathway / response to cAMP / ionotropic glutamate receptor signaling pathway / positive regulation of endothelial cell migration / response to hormone / positive regulation of synaptic transmission, glutamatergic / response to cocaine / positive regulation of translation / integrin-mediated signaling pathway / response to ischemia / long-term synaptic potentiation / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / positive regulation of JNK cascade / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / response to hydrogen peroxide / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / response to calcium ion / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / positive regulation of nitric oxide biosynthetic process / MAPK cascade / neuron projection development / lamellipodium / presynapse / regulation of cell shape / cell cortex / positive regulation of cytosolic calcium ion concentration / growth cone / cell body / positive regulation of cell growth / protein tyrosine kinase activity / protein-containing complex assembly / response to ethanol / negative regulation of neuron apoptotic process / protein autophosphorylation / adaptive immune response / dendritic spine / positive regulation of ERK1 and ERK2 cascade / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / cell surface receptor signaling pathway / response to hypoxia / positive regulation of cell migration
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. / 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
Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.71 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.547, 82.547, 139.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 3.4 M NaCl, 100 mM HEPES, 1% glycerol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1000, 0.9795, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2005
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97951
30.97961
ReflectionResolution: 2.7→50 Å / Num. obs: 6817 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 95.9 Å2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99.3

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.71→40.52 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 225706.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.295 715 10.8 %RANDOM
Rwork0.261 ---
obs0.261 6596 95.7 %-
all-6817 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 92.5371 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 105.3 Å2
Baniso -1Baniso -2Baniso -3
1-10.37 Å20 Å20 Å2
2--10.37 Å20 Å2
3----20.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.71→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 0 0 909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 83 8.9 %
Rwork0.335 850 -
obs--83.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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