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- PDB-4xef: Pyk2-FAT complexed with Leupaxin LD motif LD1 -

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Basic information

Entry
Database: PDB / ID: 4xef
TitlePyk2-FAT complexed with Leupaxin LD motif LD1
Components
  • 20-mer peptide containing LD1 motif of leupaxin
  • Protein-tyrosine kinase 2-beta
KeywordsCELL ADHESION / 4-HELIX BUNDLE / FOCAL ADHESION / TYROSINE KINASE / LEUPAXIN
Function / homology
Function and homology information


negative regulation of B cell receptor signaling pathway / regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / muscle structure development / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway ...negative regulation of B cell receptor signaling pathway / regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / muscle structure development / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / regulation of postsynaptic density assembly / blood vessel endothelial cell migration / negative regulation of muscle cell apoptotic process / negative regulation of bone mineralization / muscle alpha-actinin binding / cortical cytoskeleton organization / apical dendrite / positive regulation of ubiquitin-dependent protein catabolic process / regulation of release of sequestered calcium ion into cytosol / activation of Janus kinase activity / cellular response to fluid shear stress / negative regulation of cell adhesion / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / podosome / NMDA selective glutamate receptor complex / Interleukin-2 signaling / sprouting angiogenesis / long-term synaptic depression / oocyte maturation / Signal regulatory protein family interactions / positive regulation of cell-matrix adhesion / calmodulin-dependent protein kinase activity / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of actin filament polymerization / stress fiber assembly / filamentous actin / regulation of cell adhesion mediated by integrin / negative regulation of potassium ion transport / positive regulation of excitatory postsynaptic potential / RHOU GTPase cycle / response to immobilization stress / endothelial cell migration / positive regulation of protein kinase activity / postsynaptic density, intracellular component / glial cell proliferation / glutamate receptor binding / cellular defense response / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / response to glucose / response to mechanical stimulus / cellular response to retinoic acid / stress fiber / peptidyl-tyrosine autophosphorylation / bone resorption / response to cAMP / tumor necrosis factor-mediated signaling pathway / ionotropic glutamate receptor signaling pathway / positive regulation of endothelial cell migration / positive regulation of synaptic transmission, glutamatergic / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / response to hormone / response to cocaine / positive regulation of translation / cell projection / integrin-mediated signaling pathway / response to ischemia / long-term synaptic potentiation / regulation of actin cytoskeleton organization / transcription coregulator activity / adherens junction / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / Z disc / response to calcium ion / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / : / neuron projection development / positive regulation of reactive oxygen species metabolic process / MAPK cascade / positive regulation of nitric oxide biosynthetic process / presynapse / lamellipodium / actin binding / heart development / cell cortex / regulation of cell shape
Similarity search - Function
Leupaxin/Paxillin/TGFB1I1 / 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 ...Leupaxin/Paxillin/TGFB1I1 / 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
Leupaxin / Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMiller, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100909-03 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural Basis for the Interaction between Pyk2-FAT Domain and Leupaxin LD Repeats.
Authors: Vanarotti, M.S. / Finkelstein, D.B. / Guibao, C.D. / Nourse, A. / Miller, D.J. / Zheng, J.J.
History
DepositionDec 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Mar 16, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine kinase 2-beta
B: 20-mer peptide containing LD1 motif of leupaxin
C: 20-mer peptide containing LD1 motif of leupaxin
D: Protein-tyrosine kinase 2-beta
E: 20-mer peptide containing LD1 motif of leupaxin
F: 20-mer peptide containing LD1 motif of leupaxin


Theoretical massNumber of molelcules
Total (without water)39,8076
Polymers39,8076
Non-polymers00
Water21612
1
A: Protein-tyrosine kinase 2-beta
B: 20-mer peptide containing LD1 motif of leupaxin
C: 20-mer peptide containing LD1 motif of leupaxin


Theoretical massNumber of molelcules
Total (without water)19,9043
Polymers19,9043
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-19 kcal/mol
Surface area8580 Å2
MethodPISA
2
D: Protein-tyrosine kinase 2-beta
E: 20-mer peptide containing LD1 motif of leupaxin
F: 20-mer peptide containing LD1 motif of leupaxin


Theoretical massNumber of molelcules
Total (without water)19,9043
Polymers19,9043
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-16 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.482, 78.094, 165.418
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 / Calcium-dependent tyrosine kinase / CADTK / Calcium-regulated non-receptor proline-rich tyrosine ...Calcium-dependent tyrosine kinase / CADTK / Calcium-regulated non-receptor proline-rich tyrosine kinase / Cell adhesion kinase beta / CAKB / Focal adhesion kinase 2 / FADK 2 / Proline-rich tyrosine kinase 2 / Related adhesion focal tyrosine kinase / RAFTK


Mass: 15228.520 Da / Num. of mol.: 2 / Fragment: FAT domain (UNP residues 871-1005) / Mutation: C899S, C972A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2B, FAK2, PYK2, RAFTK / Production host: Escherichia coli (E. coli)
References: UniProt: Q14289, non-specific protein-tyrosine kinase
#2: Protein/peptide
20-mer peptide containing LD1 motif of leupaxin


Mass: 2337.492 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O60711*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 400 nl drop contained 200 nl protein/LD1 peptide mixture (20 mM MES, pH 6.2, 1 mM protein, and 2 mM peptide) and 200 nl well solution (100 mM Tris, pH 8.5, 0.2 M MgCl2, and 30% PEG 4000).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9712 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9712 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 12937 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rsym value: 0.09 / Net I/σ(I): 20.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.2 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GM3

3gm3


Resolution: 2.5→24.83 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 690 5.36 %
Rwork0.224 --
obs0.227 12885 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 0 12 2442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092438
X-RAY DIFFRACTIONf_angle_d1.1383302
X-RAY DIFFRACTIONf_dihedral_angle_d15.632916
X-RAY DIFFRACTIONf_chiral_restr0.044431
X-RAY DIFFRACTIONf_plane_restr0.004421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.68770.2961250.25662181X-RAY DIFFRACTION91
2.6877-2.95780.28561290.25122439X-RAY DIFFRACTION100
2.9578-3.38480.26751500.24752451X-RAY DIFFRACTION100
3.3848-4.2610.28811440.21462475X-RAY DIFFRACTION100
4.261-24.83180.23721420.20682649X-RAY DIFFRACTION100
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)
11.7317-0.10520.09752.0501-0.29782.8096-0.0110.01280.01960.07350.0668-0.2027-0.29980.69890.03760.2649-0.05710.02610.276-0.00330.332815.42116.627518.0353
20.9987-0.47590.57560.999-0.50772.8883-0.0247-0.2140.10280.2364-0.00180.0964-0.5723-0.6820.02170.390.00780.02050.3855-0.03060.39874.938821.195623.8892
31.8071-0.592-0.07791.60050.18623.19880.18260.0082-0.19140.1499-0.0541-0.05820.629-0.3545-0.0260.2568-0.07970.04740.28440.01770.34396.50111.94619.7552
41.9392-0.0113-0.16162.5443-0.54852.07180.1044-0.1283-0.16150.0697-0.0788-0.2927-0.12840.6476-0.02620.1827-0.0509-0.00130.32150.00020.298127.061952.52711.4863
51.91360.081.18751.63270.39494.39890.0172-0.48850.05570.1053-0.20050.1623-0.6838-0.5603-0.08710.383-0.03920.0070.3505-0.01290.29116.877357.86918.2989
60.82940.14330.44952.12930.72974.45310.5156-0.3585-0.53270.2197-0.0471-0.25790.6133-0.3191-0.1090.2841-0.1007-0.00740.36160.03160.352619.243548.446716.3146
71.2657-0.3496-0.75550.27750.1670.3970.07570.4750.62310.9670.0861-0.3842-1.1060.08570.14870.89830.07490.02920.4438-0.01060.72129.359730.737121.3524
83.2783-0.0575-0.14931.75920.06834.06840.2616-0.2764-0.72810.063-0.138-0.32510.77440.3722-0.02460.59920.00780.05870.36780.13620.723515.53284.178620.6665
94.35251.7681-0.75267.66292.65395.20030.1465-0.32420.53420.2232-0.56390.4886-0.68440.28180.56520.5391-0.03280.06820.30960.00140.357220.312567.087814.3634
101.65120.38821.10532.16470.9491.22590.0056-0.6555-0.3116-0.00350.2261-0.06190.77340.3961-0.03720.5979-0.0728-0.05490.66350.18660.947827.75440.287917.485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 870 THROUGH 928 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 929 THROUGH 968 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 969 THROUGH 1005 )
4X-RAY DIFFRACTION4CHAIN 'D' AND (RESID 871 THROUGH 932 )
5X-RAY DIFFRACTION5CHAIN 'D' AND (RESID 933 THROUGH 966 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 967 THROUGH 1004 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 1 THROUGH 13 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 1 THROUGH 15 )
9X-RAY DIFFRACTION9CHAIN 'F' AND (RESID 2 THROUGH 13 )
10X-RAY DIFFRACTION10CHAIN 'E' AND (RESID 1 THROUGH 15 )

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