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- PDB-6wlx: PAK4 kinase domain in complex with beta-catenin Ser675 substrate ... -

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Basic information

Entry
Database: PDB / ID: 6wlx
TitlePAK4 kinase domain in complex with beta-catenin Ser675 substrate peptide
Components
  • Catenin beta-1
  • Serine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / serine/threonine kinase PAK4 / beta-catenin / phosphopeptide / Ser675
Function / homology
Function and homology information


CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation ...CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / mesenchymal stem cell differentiation / beta-catenin-ICAT complex / metanephros morphogenesis / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / neural plate development / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / negative regulation of mitotic cell cycle, embryonic / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / regulation of timing of anagen / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / Specification of the neural plate border / embryonic axis specification / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / Formation of the nephric duct / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / sympathetic ganglion development / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of skeletal muscle tissue development / cranial skeletal system development / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / endothelial tube morphogenesis / positive regulation of odontoblast differentiation / presynaptic active zone cytoplasmic component / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / dendritic spine development / alpha-catenin binding / cadherin binding involved in cell-cell adhesion / establishment of blood-brain barrier / Germ layer formation at gastrulation / negative regulation of oligodendrocyte differentiation / male genitalia development / fascia adherens / flotillin complex / apicolateral plasma membrane / epithelial cell proliferation involved in prostate gland development / epithelial cell differentiation involved in prostate gland development / Formation of definitive endoderm / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / embryonic brain development / beta-catenin destruction complex / oocyte development / adherens junction assembly / lung-associated mesenchyme development / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / Formation of axial mesoderm / negative regulation of protein sumoylation / embryonic heart tube development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated
Similarity search - Function
Beta-catenin / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat ...Beta-catenin / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PAK 4 / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsChetty, A.K. / Ha, B.H. / Boggon, T.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102262 United States
American Heart Association19IPLOI34740007 United States
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Recognition of physiological phosphorylation sites by p21-activated kinase 4.
Authors: Chetty, A.K. / Sexton, J.A. / Ha, B.H. / Turk, B.E. / Boggon, T.J.
History
DepositionApr 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 12, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Oct 18, 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: Serine/threonine-protein kinase PAK 4
B: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)39,9852
Polymers39,9852
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-2 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.605, 61.605, 179.402
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 39123.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Production host: Escherichia coli (E. coli)
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Protein/peptide Catenin beta-1 / Beta-catenin


Mass: 862.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35222
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl, 2M Na acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, 5mM peptide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 18577 / % possible obs: 99.9 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.032 / Rrim(I) all: 0.11 / Χ2: 1.113 / Net I/σ(I): 8 / Num. measured all: 208953
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.2811.81.1517990.7010.3471.2020.932100
2.28-2.3711.40.8718190.7830.2670.9121.01100
2.37-2.4810.10.718070.8410.2280.7381.081100
2.48-2.6110.40.51218160.9080.1640.5381.05599.9
2.61-2.7712.70.36718170.9630.1070.3821.096100
2.77-2.9912.20.2518330.9820.0740.2611.23999.9
2.99-3.2911.50.15418580.9930.0470.1621.29699.9
3.29-3.769.60.10418640.9940.0350.111.23499.9
3.76-4.7412.30.07419130.9980.0220.0771.19399.9
4.74-5010.40.05720510.9980.0180.060.98399.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIJ

4fij


Resolution: 2.2→44.85 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 919 5 %
Rwork0.1967 17447 -
obs0.1984 18366 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.73 Å2 / Biso mean: 56.5011 Å2 / Biso min: 29.65 Å2
Refinement stepCycle: final / Resolution: 2.2→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 0 54 2404
Biso mean---49.53 -
Num. residues----297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.320.35211270.294724192546
2.32-2.460.34781290.282724452574
2.46-2.650.30261280.256824292557
2.65-2.920.30261300.245924642594
2.92-3.340.25371300.222624762606
3.34-4.210.22481330.177125212654
4.21-44.850.17171420.158226932835
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)
12.06421.49390.05962.69670.44652.6571-0.03560.121-0.1781-0.23340.05980.26410.3457-0.0278-0.01070.44290.0255-0.07770.28130.0410.450514.2033-11.53222.7458
22.49831.3821-0.7924.7113-0.36022.5084-0.13590.22770.0384-0.50570.14880.10040.0557-0.03170.00340.36020.0004-0.00980.33270.06080.367321.5886-9.0276-0.964
30.04770.01020.01350.0020.00280.0037-0.1326-0.2097-0.2443-0.09030.03580.28620.0666-0.42490.09080.9283-0.14110.18920.63110.01520.86748.0583-6.34533.7061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 299 through 395 )A299 - 395
2X-RAY DIFFRACTION2chain 'A' and (resid 396 through 590 )A396 - 590
3X-RAY DIFFRACTION3chain 'B' and (resid 672 through 676 )B672 - 676

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