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- PDB-3u3f: Structural basis for the interaction of Pyk2 PAT domain with paxi... -

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Basic information

Entry
Database: PDB / ID: 3u3f
TitleStructural basis for the interaction of Pyk2 PAT domain with paxillin LD motifs
Components
  • Paxillin LD2 peptide
  • Protein-tyrosine kinase 2-beta
KeywordsTRANSFERASE/signaling protein / 4-helix bundle / focal adhesion / tyrosine kinase / paxillin / TRANSFERASE-signaling protein complex
Function / homology
Function and homology information


regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / regulation of ubiquitin-dependent protein catabolic process / 3-phosphoinositide-dependent protein kinase binding / endothelin receptor signaling pathway / regulation of postsynaptic density assembly ...regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / regulation of ubiquitin-dependent protein catabolic process / 3-phosphoinositide-dependent protein kinase binding / endothelin receptor signaling pathway / regulation of postsynaptic density assembly / negative regulation of myeloid cell differentiation / blood vessel endothelial cell migration / negative regulation of bone mineralization / negative regulation of muscle cell apoptotic process / vinculin binding / cortical cytoskeleton organization / neuropilin binding / apical dendrite / oocyte maturation / positive regulation of ubiquitin-dependent protein catabolic process / activation of Janus kinase activity / regulation of release of sequestered calcium ion into cytosol / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / calmodulin-dependent protein kinase activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / sprouting angiogenesis / Interleukin-2 signaling / long-term synaptic depression / microtubule associated complex / positive regulation of cell-matrix adhesion / Signal regulatory protein family interactions / growth hormone receptor signaling pathway / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of actin filament polymerization / stress fiber assembly / postsynaptic density, intracellular component / regulation of NMDA receptor activity / positive regulation of excitatory postsynaptic potential / negative regulation of potassium ion transport / RHOU GTPase cycle / response to immobilization stress / endothelial cell migration / Smooth Muscle Contraction / positive regulation of protein kinase activity / glial cell proliferation / GAB1 signalosome / cellular defense response / response to glucose / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / response to mechanical stimulus / regulation of cell adhesion / stress fiber / cellular response to retinoic acid / peptidyl-tyrosine autophosphorylation / bone resorption / positive regulation of stress fiber assembly / response to cAMP / tumor necrosis factor-mediated signaling pathway / ionotropic glutamate receptor signaling pathway / response to hormone / positive regulation of synaptic transmission, glutamatergic / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / positive regulation of endothelial cell migration / positive regulation of translation / response to cocaine / long-term synaptic potentiation / integrin-mediated signaling pathway / response to ischemia / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / regulation of synaptic plasticity / non-specific protein-tyrosine kinase / Schaffer collateral - CA1 synapse / non-membrane spanning protein tyrosine kinase activity / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / positive regulation of neuron projection development / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / response to calcium ion / peptidyl-tyrosine phosphorylation / neuron projection development / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / : / positive regulation of nitric oxide biosynthetic process / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / cell migration / presynapse / lamellipodium
Similarity search - Function
Paxillin / : / : / Paxillin family / 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 ...Paxillin / : / : / Paxillin family / 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 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
Paxillin / Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å
AuthorsVanarotti, M. / Miller, D.J. / Guibao, C.C. / Zheng, J.J.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural and Mechanistic Insights into the Interaction between Pyk2 and Paxillin LD Motifs.
Authors: Vanarotti, M.S. / Miller, D.J. / Guibao, C.D. / Nourse, A. / Zheng, J.J.
History
DepositionOct 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-tyrosine kinase 2-beta
B: Protein-tyrosine kinase 2-beta
C: Protein-tyrosine kinase 2-beta
D: Protein-tyrosine kinase 2-beta
E: Paxillin LD2 peptide
F: Paxillin LD2 peptide
G: Paxillin LD2 peptide
H: Paxillin LD2 peptide
I: Paxillin LD2 peptide
J: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)72,53310
Polymers72,53310
Non-polymers00
Water543
1
A: Protein-tyrosine kinase 2-beta
E: Paxillin LD2 peptide
I: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)19,0913
Polymers19,0913
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-19 kcal/mol
Surface area7940 Å2
MethodPISA
2
B: Protein-tyrosine kinase 2-beta
F: Paxillin LD2 peptide
J: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)19,0913
Polymers19,0913
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-16 kcal/mol
Surface area7990 Å2
MethodPISA
3
C: Protein-tyrosine kinase 2-beta
G: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)17,1762
Polymers17,1762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-7 kcal/mol
Surface area7320 Å2
MethodPISA
4
D: Protein-tyrosine kinase 2-beta
H: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)17,1762
Polymers17,1762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-10 kcal/mol
Surface area7450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.599, 83.747, 170.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein-tyrosine kinase 2-beta / Focal adhesion kinase 2 / FADK 2 / RAFTK


Mass: 15260.584 Da / Num. of mol.: 4 / Fragment: unp residues 871-1005 / Mutation: C899S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2B, FAK2, PYK2, RAFTK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14289, non-specific protein-tyrosine kinase
#2: Protein/peptide
Paxillin LD2 peptide


Mass: 1915.128 Da / Num. of mol.: 6 / Fragment: unp residues 261-277 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P49023
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.12 Å3/Da / Density % sol: 70.11 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: The 4 ul drop contained 2 ul protein-LD4 peptide mixture (20mM Mes, pH6.2, 1mM protein, 2 mM peptide) and 2 ul ML (100 mM MES pH6.3, 4.2 M NaCl, 2%(v/v) glycerol., VAPOR DIFFUSION, SITTING ...Details: The 4 ul drop contained 2 ul protein-LD4 peptide mixture (20mM Mes, pH6.2, 1mM protein, 2 mM peptide) and 2 ul ML (100 mM MES pH6.3, 4.2 M NaCl, 2%(v/v) glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 291.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2011 / Details: mirrors
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 22414 / Num. obs: 21900 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 106.2 Å2 / Rsym value: 0.06 / Net I/σ(I): 25.8
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 2076 / Rsym value: 0.647 / % possible all: 94.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERMolecular Replacementphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3GM1

3gm1


Resolution: 3.101→29.848 Å / SU ML: 0.3 / σ(F): 0.08 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 1045 5.01 %Random
Rwork0.218 ---
obs0.2204 20847 93.3 %-
all-20847 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.391 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0616 Å20 Å2-0 Å2
2--3.1061 Å20 Å2
3----2.0445 Å2
Refinement stepCycle: LAST / Resolution: 3.101→29.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 0 3 4292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084307
X-RAY DIFFRACTIONf_angle_d1.0655844
X-RAY DIFFRACTIONf_dihedral_angle_d18.212738
X-RAY DIFFRACTIONf_chiral_restr0.061768
X-RAY DIFFRACTIONf_plane_restr0.004743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.101-3.26430.35891090.31052385X-RAY DIFFRACTION81
3.2643-3.46860.33271550.26652783X-RAY DIFFRACTION93
3.4686-3.73590.28571370.24892822X-RAY DIFFRACTION94
3.7359-4.1110.25261560.20552875X-RAY DIFFRACTION96
4.111-4.70390.24551700.17512954X-RAY DIFFRACTION98
4.7039-5.91880.28781560.2172960X-RAY DIFFRACTION97
5.9188-29.84950.23841620.20433023X-RAY DIFFRACTION95

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