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- PDB-4xbr: In cellulo Crystal Structure of PAK4 in complex with Inka -

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Basic information

Entry
Database: PDB / ID: 4xbr
TitleIn cellulo Crystal Structure of PAK4 in complex with Inka
ComponentsProtein FAM212A,Serine/threonine-protein kinase PAK 4
KeywordsPeptide / Transferase / PAK4 / Inka / Crystallization
Function / homology
Function and homology information


dendritic spine development / cadherin binding involved in cell-cell adhesion / protein serine/threonine kinase inhibitor activity / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / protein serine/threonine kinase inhibitor activity / 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 / RAC2 GTPase cycle / RAC3 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 / intracellular signal transduction / protein kinase activity / cell cycle / phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / protein kinase binding / Golgi apparatus / signal transduction / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
FAM212 domain / PAK4-inhibitor inka / FAM212 family / 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 ...FAM212 domain / PAK4-inhibitor inka / FAM212 family / 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
ADENOSINE-5'-TRIPHOSPHATE / Serine/threonine-protein kinase PAK 4 / PAK4-inhibitor INKA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsBaskaran, Y. / Ang, K.C. / Anekal, P.V. / Chan, W.L. / Grimes, J.M. / Manser, E. / Robinson, R.C.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Agency for Science, Technology and Research Singapore
CitationJournal: Nat Commun / Year: 2015
Title: An in cellulo-derived structure of PAK4 in complex with its inhibitor Inka1
Authors: Baskaran, Y. / Ang, K.C. / Anekal, P.V. / Chan, W.L. / Grimes, J.M. / Manser, E. / Robinson, R.C.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein FAM212A,Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8034
Polymers41,2471
Non-polymers5563
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-23 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.040, 144.040, 62.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Protein FAM212A,Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 41247.383 Da / Num. of mol.: 1 / Fragment: UNP residues 166-203,UNP residues 278-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM212A, C3orf54, PAK4, KIAA1142 / Cell (production host): Kidney cell CRL-1651 / Cell line (production host): COS-7 / Production host: Chlorocebus aethiops (grivet)
References: UniProt: Q96EL1, UniProt: O96013, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74.39 % / Description: Hexagonal rod
Crystal growTemperature: 310.15 K / Method: in cell / Details: In cellulo growth

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.94→44.2 Å / Num. obs: 15517 / % possible obs: 97.3 % / Redundancy: 7.8 % / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
xia20.3.6.0data reduction
xia20.3.6.0data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIE

4fie


Resolution: 2.94→44.2 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.215 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22973 776 5 %RANDOM
Rwork0.18909 ---
obs0.19113 14702 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.705 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.94→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 33 0 2536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192586
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9973509
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3935314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62123.246114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32715458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5511524
X-RAY DIFFRACTIONr_chiral_restr0.0920.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211921
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.941→3.018 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 44 -
Rwork0.321 906 -
obs--82.54 %

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