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- PDB-3e7o: Crystal Structure of JNK2 -

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Basic information

Entry
Database: PDB / ID: 3e7o
TitleCrystal Structure of JNK2
ComponentsMitogen-activated protein kinase 9
KeywordsTRANSFERASE / MAP kinase insert / activation loop / indazole inhibitor / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


protein localization to tricellular tight junction / JUN kinase activity / inflammatory response to wounding / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / mitogen-activated protein kinase / JNK cascade ...protein localization to tricellular tight junction / JUN kinase activity / inflammatory response to wounding / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / mitogen-activated protein kinase / JNK cascade / cellular response to cadmium ion / protein serine/threonine/tyrosine kinase activity / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of protein ubiquitination / apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / FCERI mediated MAPK activation / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / regulation of circadian rhythm / cellular response to reactive oxygen species / cellular senescence / Signaling by ALK fusions and activated point mutants / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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
Chem-35F / Mitogen-activated protein kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsKuglstatter, A. / Villasenor, A.G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The crystal structure of JNK2 reveals conformational flexibility in the MAP kinase insert and indicates its involvement in the regulation of catalytic activity.
Authors: Shaw, D. / Wang, S.M. / Villasenor, A.G. / Tsing, S. / Walter, D. / Browner, M.F. / Barnett, J. / Kuglstatter, A.
History
DepositionAug 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 30, 2014Group: Data collection
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Mitogen-activated protein kinase 9
B: Mitogen-activated protein kinase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2844
Polymers82,5432
Non-polymers7412
Water4,522251
1
A: Mitogen-activated protein kinase 9
hetero molecules

B: Mitogen-activated protein kinase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2844
Polymers82,5432
Non-polymers7412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1390 Å2
ΔGint-9 kcal/mol
Surface area32420 Å2
MethodPISA
2
A: Mitogen-activated protein kinase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6422
Polymers41,2711
Non-polymers3701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Mitogen-activated protein kinase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6422
Polymers41,2711
Non-polymers3701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.688, 78.784, 78.927
Angle α, β, γ (deg.)90.00, 96.43, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains two biological units which differ in conformation.

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Components

#1: Protein Mitogen-activated protein kinase 9 / Stress-activated protein kinase JNK2 / c-Jun N-terminal kinase 2 / JNK-55


Mass: 41271.430 Da / Num. of mol.: 2 / Fragment: residues 7-362 / Mutation: C177S, C222S, K250A, K251A, K265A, K270A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK9, JNK2, PRKM9 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45984, mitogen-activated protein kinase
#2: Chemical ChemComp-35F / N-{3-[5-(1H-1,2,4-triazol-3-yl)-1H-indazol-3-yl]phenyl}furan-2-carboxamide


Mass: 370.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H14N6O2
#3: Water ChemComp-HOH / 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: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M MES, 0.6M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. all: 53458 / Num. obs: 51687 / % possible obs: 96.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 8.4
Reflection shellResolution: 2.14→2.23 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4473 / Rsym value: 0.468 / % possible all: 84

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JNK

1jnk


Resolution: 2.14→44.29 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.335 / SU ML: 0.14 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25031 2624 5.1 %RANDOM
Rwork0.21697 ---
obs0.21868 49061 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.52 Å2
2--0.31 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.14→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5384 0 56 251 5691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225569
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9747548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1995660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94824.217249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27115984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6051530
X-RAY DIFFRACTIONr_chiral_restr0.0750.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024167
X-RAY DIFFRACTIONr_nbd_refined0.1850.22376
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23793
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.212
X-RAY DIFFRACTIONr_mcbond_it0.6831.53450
X-RAY DIFFRACTIONr_mcangle_it1.16625433
X-RAY DIFFRACTIONr_scbond_it1.34432453
X-RAY DIFFRACTIONr_scangle_it2.1824.52115
LS refinement shellResolution: 2.143→2.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 131 -
Rwork0.275 2459 -
obs--65.31 %

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