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- PDB-9m41: The crystal structure of full-length PAK2 containing K278R and D3... -

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Basic information

Entry
Database: PDB / ID: 9m41
TitleThe crystal structure of full-length PAK2 containing K278R and D368N mutants
ComponentsSerine/threonine-protein kinase PAK 2
KeywordsTRANSFERASE / inactive PAK2
Function / homology
Function and homology information


Regulation of PAK-2p34 activity by PS-GAP/RHG10 / protein localization to cell-cell junction / Stimulation of the cell death response by PAK-2p34 / dendritic spine development / bicellular tight junction assembly / cardiac muscle hypertrophy / Nef and signal transduction / adherens junction assembly / Activation of RAC1 / positive regulation of extrinsic apoptotic signaling pathway ...Regulation of PAK-2p34 activity by PS-GAP/RHG10 / protein localization to cell-cell junction / Stimulation of the cell death response by PAK-2p34 / dendritic spine development / bicellular tight junction assembly / cardiac muscle hypertrophy / Nef and signal transduction / adherens junction assembly / Activation of RAC1 / positive regulation of extrinsic apoptotic signaling pathway / Ephrin signaling / CD28 dependent Vav1 pathway / negative regulation of stress fiber assembly / regulation of axonogenesis / RHOV GTPase cycle / RHOJ GTPase cycle / regulation of cytoskeleton organization / stimulatory C-type lectin receptor signaling pathway / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / protein tyrosine kinase activator activity / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / Generation of second messenger molecules / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / Smooth Muscle Contraction / RAC2 GTPase cycle / RAC3 GTPase cycle / vascular endothelial growth factor receptor signaling pathway / cellular response to transforming growth factor beta stimulus / negative regulation of protein kinase activity / Regulation of activated PAK-2p34 by proteasome mediated degradation / RAC1 GTPase cycle / CD209 (DC-SIGN) signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / secretory granule / cellular response to starvation / VEGFR2 mediated vascular permeability / MAPK6/MAPK4 signaling / FCERI mediated MAPK activation / small GTPase binding / VEGFA-VEGFR2 Pathway / cell-cell junction / cell migration / protein autophosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / nuclear speck / intracellular signal transduction / cadherin binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p21-activated kinase 2, catalytic domain / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...p21-activated kinase 2, catalytic domain / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Serine/threonine-protein kinase PAK 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsHu, H.-F. / Luo, Z.P. / Wu, J.-W. / Wang, Z.-X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Ministry of Science and Technology (MoST, China) China
CitationJournal: Structure / Year: 2025
Title: Crystal structures of PAK2 reveal new insights into its autoinhibitory mechanism.
Authors: Hu, H.F. / Luo, Z. / Zhang, Y. / Fang, X. / Zhu, Z. / Wu, J.W. / Wang, Z.X.
History
DepositionMar 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 2
B: Serine/threonine-protein kinase PAK 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3053
Polymers121,2102
Non-polymers951
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.824, 55.844, 146.407
Angle α, β, γ (deg.)90.000, 105.435, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Serine/threonine-protein kinase PAK 2 / Gamma-PAK / PAK65 / S6/H4 kinase / p21-activated kinase 2 / PAK-2 / p58


Mass: 60605.191 Da / Num. of mol.: 2 / Mutation: K278R D368N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13177, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 3350, 0.1M Na/K phosphate pH 6.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 17583 / % possible obs: 95.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 82.72 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.162 / Net I/σ(I): 9.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1786 / CC1/2: 0.49 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIXv2.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→50 Å / SU ML: 0.3712 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2437 826 4.7 %
Rwork0.2042 16757 -
obs0.2061 17583 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.72 Å2
Refinement stepCycle: LAST / Resolution: 3.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5358 0 5 2 5365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00865454
X-RAY DIFFRACTIONf_angle_d1.16947378
X-RAY DIFFRACTIONf_chiral_restr0.0578854
X-RAY DIFFRACTIONf_plane_restr0.0083946
X-RAY DIFFRACTIONf_dihedral_angle_d15.43662078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.210.26871090.21992422X-RAY DIFFRACTION79.67
3.21-3.460.3191420.26142891X-RAY DIFFRACTION96.72
3.46-3.810.31321510.25762796X-RAY DIFFRACTION94.24
3.81-4.360.26691290.21412837X-RAY DIFFRACTION93.3
4.36-5.490.20991350.17682926X-RAY DIFFRACTION95.96
5.49-500.20811600.18012885X-RAY DIFFRACTION92.81

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