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- PDB-6wly: PAK4 kinase domain in complex with LIMK1 Thr508 substrate peptide -

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Basic information

Entry
Database: PDB / ID: 6wly
TitlePAK4 kinase domain in complex with LIMK1 Thr508 substrate peptide
Components
  • LIM Kinase 1 peptide
  • Serine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / serine/threonine kinase PAK4 / LIM kinase 1 / LIMK1 / phosphopeptide / Thr508
Function / homology
Function and homology information


positive regulation of actin filament bundle assembly / dendritic spine development / cadherin binding involved in cell-cell adhesion / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Activation of RAC1 / RHOV GTPase cycle / Fc-gamma receptor signaling pathway involved in phagocytosis ...positive regulation of actin filament bundle assembly / dendritic spine development / cadherin binding involved in cell-cell adhesion / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Activation of RAC1 / RHOV GTPase cycle / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHOJ GTPase cycle / RHOQ GTPase cycle / RHO GTPases activate PAKs / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / cellular response to organic cyclic compound / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of axon extension / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / positive regulation of stress fiber assembly / RAC1 GTPase cycle / EPHB-mediated forward signaling / heat shock protein binding / male germ cell nucleus / regulation of cell growth / adherens junction / Regulation of actin dynamics for phagocytic cup formation / positive regulation of angiogenesis / cell migration / lamellipodium / nervous system development / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / intracellular signal transduction / nuclear speck / cell cycle / phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type ...p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / LIM domain kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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: LIM Kinase 1 peptide


Theoretical massNumber of molelcules
Total (without water)40,3482
Polymers40,3482
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-5 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.626, 61.626, 179.596
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 BL21(DE3) (bacteria)
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Protein/peptide LIM Kinase 1 peptide / LIMK-1


Mass: 1224.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P53667, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.11 Å3/Da / Density % sol: 41.79 %
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, 2mM 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: Jul 7, 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: 1.9→50 Å / Num. obs: 28404 / % possible obs: 99.9 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.03 / Rrim(I) all: 0.143 / Χ2: 0.984 / Net I/σ(I): 6.8 / Num. measured all: 576393
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9715.31.50227470.6150.3861.5530.83799.9
1.97-2.0520.31.05427780.8640.2321.080.67699.9
2.05-2.1421.50.75627950.9430.1610.7740.73799.9
2.14-2.2520.10.62327700.9520.1380.6391.04199.9
2.25-2.3920.10.41227960.9780.0910.4231.03499.8
2.39-2.5819.30.29128330.9830.0660.2991.065100
2.58-2.8417.30.20128130.9910.0490.2071.09899.8
2.84-3.2523.80.13928660.9970.0290.1421.126100
3.25-4.0923.90.10229000.9980.0210.1051.071100
4.09-5020.90.12231060.9960.0270.1251.08399.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.57 Å43.58 Å
Translation5.57 Å43.58 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
Cootmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIJ

4fij


Resolution: 1.9→43.58 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 1412 5 %
Rwork0.1861 26816 -
obs0.1871 28228 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.1 Å2 / Biso mean: 45.0861 Å2 / Biso min: 28.98 Å2
Refinement stepCycle: final / Resolution: 1.9→43.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 0 135 2518
Biso mean---47.85 -
Num. residues----301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.970.32071380.315126212759
1.97-2.050.30241380.257126222760
2.05-2.140.24021380.233626202758
2.14-2.250.25731370.235926172754
2.25-2.390.28091410.226926592800
2.39-2.580.26251400.222126672807
2.58-2.840.22841400.206826622802
2.84-3.250.22161430.204327092852
3.25-4.090.1881430.159927342877
4.09-43.580.161540.153229053059
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)
13.31481.95490.49833.88380.33952.874-0.02770.0523-0.1241-0.0277-0.03450.11230.19430.04510.04690.28720.0332-0.02240.19880.01710.268814.3959-11.308222.8016
22.16841.126-0.53174.5957-0.01372.1279-0.07030.20540.0911-0.40740.09630.07960.0234-0.0332-0.02710.26320.0096-0.00210.25410.06650.255821.7098-8.8224-0.7617
37.90055.2934-3.78222.002-5.82688.23290.2363-0.31290.01510.18650.18672.4534-0.0058-1.2738-0.4120.4129-0.00790.05990.56550.08840.8876.3727-9.39374.3537
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 504 through 512 )B504 - 512

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