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- PDB-2q0n: Structure of human p21 activating kinase 4 (PAK4) in complex with... -

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Basic information

Entry
Database: PDB / ID: 2q0n
TitleStructure of human p21 activating kinase 4 (PAK4) in complex with a consensus peptide
Components
  • Serine/threonine-protein kinase PAK 4
  • Synthetic peptidePeptide synthesis
KeywordsTRANSFERASE / PROTEIN KINASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / PAK4 / STE20 / KINASE / ATP-BINDING / SERINE/THREONINE-PROTEIN KINASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / RHOG GTPase cycle / cellular response to organic cyclic compound / RAC3 GTPase cycle / RAC2 GTPase cycle / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / RAC1 GTPase cycle / regulation of cell growth / adherens junction / positive regulation of angiogenesis / cell migration / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cell cycle / phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFilippakopoulos, P. / Eswaran, J. / Turnbull, A. / Papagrigoriou, E. / Pike, A.W. / von Delft, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. ...Filippakopoulos, P. / Eswaran, J. / Turnbull, A. / Papagrigoriou, E. / Pike, A.W. / von Delft, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of human p21 activating kinase 4 (PAK4) in complex with a consensus peptide.
Authors: Filippakopoulos, P. / Eswaran, J. / Turnbull, A. / Papagrigoriou, E. / Pike, A.W. / von Delft, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Knapp, S.
History
DepositionMay 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,24411
Polymers35,6512
Non-polymers5939
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.678, 145.678, 39.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-111-

HOH

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Components

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


Mass: 34091.566 Da / Num. of mol.: 1 / Fragment: Kinase domain, residues 291-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-R3
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Protein/peptide Synthetic peptide / Peptide synthesis


Mass: 1559.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.7M Ammonium sulfate, 15% PEG400, 1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 12 % / Av σ(I) over netI: 16.3 / Number: 486051 / Rmerge(I) obs: 0.057 / Χ2: 1.05 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 40410 / % possible obs: 92.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.775093.710.0371.0912.6
2.993.7786.610.0511.07113.3
2.612.9910010.0531.07514.1
2.382.6110010.0651.01114.1
2.22.3865.510.0921.04912
2.072.210010.1131.04214.1
1.972.0710010.151.00213.9
1.891.9784.810.2181.07110
1.811.8999.710.2891.0619.8
1.751.8194.210.3551.0465.6
ReflectionResolution: 1.75→50 Å / Num. all: 43686 / Num. obs: 40410 / % possible obs: 92.5 % / Redundancy: 12 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Χ2: 1.05 / Net I/σ(I): 16.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.355 / Num. unique all: 4036 / Χ2: 1.046 / % possible all: 94.2

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å32.57 Å
Translation2.5 Å32.57 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2J0I

2j0i


Resolution: 1.75→32.58 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.673 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2020 5 %RANDOM
Rwork0.182 ---
obs0.185 40359 92.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.143 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 37 251 2667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222523
X-RAY DIFFRACTIONr_bond_other_d0.0020.021755
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9823425
X-RAY DIFFRACTIONr_angle_other_deg1.01134272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14723.084107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87115.035433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7731522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
X-RAY DIFFRACTIONr_nbd_refined0.2290.2498
X-RAY DIFFRACTIONr_nbd_other0.2070.21906
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21205
X-RAY DIFFRACTIONr_nbtor_other0.0880.21266
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2163
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.217
X-RAY DIFFRACTIONr_mcbond_it1.1021.51712
X-RAY DIFFRACTIONr_mcbond_other0.2941.5619
X-RAY DIFFRACTIONr_mcangle_it1.4522535
X-RAY DIFFRACTIONr_scbond_it2.30831036
X-RAY DIFFRACTIONr_scangle_it3.1824.5880
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 159 -
Rwork0.244 2792 -
obs-2951 92.89 %
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)
17.0806-1.40040.27710.40677.826713.71870.1060.6041-0.1796-0.0544-0.28950.26090.3920.13610.1835-0.19310.0411-0.03890.0381-0.0168-0.0818-65.76824.297-22.697
215.86471.76651.27050.47820.96874.11010.13490.44840.4019-0.1105-0.01030.1795-0.39640.1672-0.1246-0.1008-0.0011-0.0026-0.06840.0697-0.03-52.9438.274-17.41
32.26710.29140.48072.43770.04343.19470.03110.04510.1793-0.0850.05540.1417-0.09380.0028-0.0865-0.1550.0371-0.0308-0.0136-0.0007-0.0457-55.74129.858-13.978
41.069-0.18620.16691.5988-0.47760.90060.0522-0.0534-0.0403-0.048-0.03810.05370.0562-0.1512-0.0142-0.1016-0.0062-0.0067-0.0754-0.0071-0.0921-48.61621.132-5.276
50.59790.8161-0.04513.03560.08981.07290.0889-0.1406-0.22010.0335-0.0961-0.51910.12530.07490.0071-0.10620.0029-0.0243-0.10580.04810.0092-36.8114.4770.192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA298 - 3128 - 22
2X-RAY DIFFRACTION2AA313 - 33323 - 43
3X-RAY DIFFRACTION3AA334 - 37444 - 84
4X-RAY DIFFRACTION4AA375 - 50385 - 213
5X-RAY DIFFRACTION5AA504 - 591214 - 301

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