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- PDB-4xev: Fusion of Pyk2-FAT domain with Leupaxin LD1 motif, complexed with... -

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Basic information

Entry
Database: PDB / ID: 4xev
TitleFusion of Pyk2-FAT domain with Leupaxin LD1 motif, complexed with Leupaxin LD4 peptide
Components
  • 19-mer peptide containing Leupaxin LD4 motif
  • Fusion protein of Protein-tyrosine kinase 2-beta FAT domain and Leupaxin LD1 motif
KeywordsCELL ADHESION / 4-HELIX BUNDLE / FOCAL ADHESION / TYROSINE KINASE / LEUPAXIN
Function / homology
Function and homology information


regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / negative regulation of B cell receptor signaling pathway / 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 macrophage chemotaxis / neurotransmitter receptor regulator activity / negative regulation of B cell receptor signaling pathway / 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 / activation of Janus kinase activity / regulation of postsynaptic density assembly / chemokine-mediated signaling pathway / apical dendrite / negative regulation of cell adhesion / 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 / podosome / peptidyl-tyrosine autophosphorylation / positive regulation of cell-matrix adhesion / regulation of cell adhesion mediated by integrin / Golgi organization / positive regulation of actin filament polymerization / negative regulation of potassium ion transport / positive regulation of protein kinase activity / RHOU GTPase cycle / signaling receptor activator activity / positive regulation of excitatory postsynaptic potential / vascular endothelial growth factor receptor signaling pathway / bone resorption / endothelial cell migration / cellular defense response / positive regulation of synaptic transmission, glutamatergic / postsynaptic density, intracellular component / regulation of cell adhesion / cellular response to retinoic acid / ionotropic glutamate receptor binding / positive regulation of endothelial cell migration / ionotropic glutamate receptor signaling pathway / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / peptidyl-tyrosine phosphorylation / tumor necrosis factor-mediated signaling pathway / integrin-mediated signaling pathway / transcription coregulator activity / cell projection / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / positive regulation of neuron projection development / regulation of synaptic plasticity / VEGFA-VEGFR2 Pathway / epidermal growth factor receptor signaling pathway / long-term synaptic potentiation / neuron migration / positive regulation of angiogenesis / presynapse / regulation of cell shape / lamellipodium / protein autophosphorylation / cell body / growth cone / protein-containing complex assembly / 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 / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / postsynaptic density / nuclear speck / positive regulation of cell migration / negative regulation of cell population proliferation / focal adhesion / neuronal cell body / positive regulation of cell population proliferation / apoptotic process / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / ATP binding / metal ion binding / nucleus / membrane / plasma membrane / cytoplasm
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 / 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
Leupaxin / Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0073 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 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 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

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Assembly

Deposited unit
A: Fusion protein of Protein-tyrosine kinase 2-beta FAT domain and Leupaxin LD1 motif
D: Fusion protein of Protein-tyrosine kinase 2-beta FAT domain and Leupaxin LD1 motif
C: 19-mer peptide containing Leupaxin LD4 motif
F: 19-mer peptide containing Leupaxin LD4 motif


Theoretical massNumber of molelcules
Total (without water)40,2504
Polymers40,2504
Non-polymers00
Water1,27971
1
A: Fusion protein of Protein-tyrosine kinase 2-beta FAT domain and Leupaxin LD1 motif
C: 19-mer peptide containing Leupaxin LD4 motif


Theoretical massNumber of molelcules
Total (without water)20,1252
Polymers20,1252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-11 kcal/mol
Surface area8640 Å2
MethodPISA
2
D: Fusion protein of Protein-tyrosine kinase 2-beta FAT domain and Leupaxin LD1 motif
F: 19-mer peptide containing Leupaxin LD4 motif


Theoretical massNumber of molelcules
Total (without water)20,1252
Polymers20,1252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-12 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.078, 79.235, 53.227
Angle α, β, γ (deg.)90.00, 117.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fusion protein of Protein-tyrosine kinase 2-beta FAT domain and Leupaxin LD1 motif


Mass: 18034.441 Da / Num. of mol.: 2 / 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 19-mer peptide containing Leupaxin LD4 motif


Mass: 2090.376 Da / Num. of mol.: 2 / 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.: 71 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: The 4 ul drop contained 2 ul protein/LD4 peptide mixture (20 mM MES pH 6.2, 1 mM protein, and 2 mM peptide) and 2 ul well solution (100 mM MES pH 6.5 and 25 % PEG 3000).

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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: Oct 30, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 25954 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.039 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.4 / % possible all: 77.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GM3

3gm3


Resolution: 2.0073→27.263 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 1275 5.19 %
Rwork0.2039 --
obs0.2064 24570 95.78 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0073→27.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 0 71 2560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072523
X-RAY DIFFRACTIONf_angle_d0.9593421
X-RAY DIFFRACTIONf_dihedral_angle_d14.176955
X-RAY DIFFRACTIONf_chiral_restr0.032443
X-RAY DIFFRACTIONf_plane_restr0.004436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0073-2.08770.42971150.35281977X-RAY DIFFRACTION74
2.0877-2.18270.35691330.28462437X-RAY DIFFRACTION91
2.1827-2.29770.29531510.23912676X-RAY DIFFRACTION100
2.2977-2.44160.2431550.21592673X-RAY DIFFRACTION100
2.4416-2.62990.24131460.20792705X-RAY DIFFRACTION100
2.6299-2.89430.25211440.22212706X-RAY DIFFRACTION100
2.8943-3.31250.28741320.22152709X-RAY DIFFRACTION100
3.3125-4.1710.22141390.18462727X-RAY DIFFRACTION100
4.171-27.2650.23121600.1812685X-RAY DIFFRACTION98
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)
12.90410.3271.26223.0943-0.91919.6407-0.1264-0.1182-0.26650.13120.3234-0.0540.1081-0.0377-0.03190.3874-0.0123-0.08410.27480.07210.47776.521812.892322.1886
20.6371-0.0816-0.08482.323-0.20458.3049-0.1955-0.30370.11670.4010.4816-0.0179-1.2973-0.9203-0.30830.45830.0836-0.0970.40080.03940.43322.54924.772719.451
30.9268-0.57911.47492.5835-2.34425.124-0.52010.26190.37140.5305-0.2536-0.4806-1.12971.28550.61220.4423-0.0951-0.14910.38990.04660.501511.146620.349719.2763
44.75720.2287-0.34783.3665-0.38155.66880.5295-0.02310.47470.82060.11720.2983-2.1578-0.9776-0.3780.61110.060.16690.37040.02560.4399-9.33231.739725.3062
51.76390.2535-0.78473.36510.17935.25520.0908-0.15310.03080.17590.0123-0.41190.03240.7183-0.15060.2511-0.0385-0.00750.3527-0.02610.4269-0.6274-8.102726.6518
61.3682-1.0088-0.97333.49571.00365.36820.09760.1950.07080.33770.25140.06460.3139-1.2119-0.31060.306-0.04670.07340.3422-0.0270.3276-9.0287-8.567123.4468
73.80810.35622.10184.43132.44672.2932-0.072-1.18060.3472-0.1852-0.6871.3684-0.496-2.67090.85380.49440.0596-0.06250.93880.11940.7908-7.056719.261821.0615
83.26620.48550.95068.5797-1.55095.67260.0839-0.2236-0.4184-0.0702-0.3027-2.02610.45661.8473-0.05230.33060.0702-0.02320.7229-0.06050.93398.1911-7.301926.2598
91.5470.3602-0.15110.6749-0.0180.0139-0.07980.25950.57860.1450.0436-0.3569-0.11370.9626-0.0131-0.0209-0.40510.09341.6454-0.7131.690819.15613.213817.2485
103.22440.1485-1.4695.4022-0.94017.9550.0750.67980.6854-0.32671.19330.925-0.6454-2.2457-0.99850.4062-0.02820.01761.10020.43360.8387-18.0969-1.650523.7156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 872 through 932 )
2X-RAY DIFFRACTION2chain 'A' and (resid 933 through 963 )
3X-RAY DIFFRACTION3chain 'A' and (resid 964 through 1007 )
4X-RAY DIFFRACTION4chain 'D' and (resid 873 through 902 )
5X-RAY DIFFRACTION5chain 'D' and (resid 903 through 962 )
6X-RAY DIFFRACTION6chain 'D' and (resid 963 through 1006 )
7X-RAY DIFFRACTION7chain 'C' and (resid 86 through 104 )
8X-RAY DIFFRACTION8chain 'F' and (resid 86 through 103 )
9X-RAY DIFFRACTION9chain 'A' and (resid 2002 through 2013 )
10X-RAY DIFFRACTION10chain 'D' and (resid 2001 through 2013 )

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