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- PDB-1ukh: Structural basis for the selective inhibition of JNK1 by the scaf... -

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Basic information

Entry
Database: PDB / ID: 1ukh
TitleStructural basis for the selective inhibition of JNK1 by the scaffolding protein JIP1 and SP600125
Components
  • 11-mer peptide from C-jun-amino-terminal kinase interacting protein 1
  • Mitogen-activated protein kinase 8 isoform 4
KeywordsTRANSFERASE / Phosphorylation
Function / homology
Function and homology information


dentate gyrus mossy fiber / JUN phosphorylation / positive regulation of cell killing / regulation of CD8-positive, alpha-beta T cell proliferation / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / JUN kinase activity ...dentate gyrus mossy fiber / JUN phosphorylation / positive regulation of cell killing / regulation of CD8-positive, alpha-beta T cell proliferation / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / JUN kinase binding / negative regulation of JNK cascade / mitogen-activated protein kinase kinase kinase binding / positive regulation of cyclase activity / histone deacetylase regulator activity / mitogen-activated protein kinase kinase binding / NRAGE signals death through JNK / positive regulation of NLRP3 inflammasome complex assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / dendritic growth cone / kinesin binding / regulation of JNK cascade / mitogen-activated protein kinase / regulation of macroautophagy / negative regulation of intrinsic apoptotic signaling pathway / response to mechanical stimulus / axonal growth cone / response to UV / protein serine/threonine kinase binding / stress-activated MAPK cascade / energy homeostasis / vesicle-mediated transport / JNK cascade / positive regulation of protein metabolic process / cellular response to cadmium ion / cellular response to amino acid starvation / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of protein binding / peptidyl-threonine phosphorylation / FCERI mediated MAPK activation / positive regulation of JNK cascade / mitochondrial membrane / regulation of circadian rhythm / histone deacetylase binding / cellular response to mechanical stimulus / cellular response to reactive oxygen species / cellular senescence / rhythmic process / Signaling by ALK fusions and activated point mutants / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to oxidative stress / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / neuron projection / positive regulation of apoptotic process / protein phosphorylation / axon / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / synapse / endoplasmic reticulum membrane / regulation of DNA-templated transcription / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / signal transduction / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
JIP1, SH3 domain / : / Mitogen-activated protein (MAP) kinase, JNK / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. ...JIP1, SH3 domain / : / Mitogen-activated protein (MAP) kinase, JNK / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / 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
Mitogen-activated protein kinase 8 / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHeo, Y.-S. / Kim, Y.K. / Sung, B.-J. / Lee, H.S. / Lee, J.I. / Seo, C.I. / Park, S.-Y. / Kim, J.H. / Hyun, Y.-L. / Jeon, Y.H. ...Heo, Y.-S. / Kim, Y.K. / Sung, B.-J. / Lee, H.S. / Lee, J.I. / Seo, C.I. / Park, S.-Y. / Kim, J.H. / Hyun, Y.-L. / Jeon, Y.H. / Ro, S. / Lee, T.G. / Cho, J.M. / Hwang, K.Y. / Yang, C.-H.
CitationJournal: Embo J. / Year: 2004
Title: Structural basis for the selective inhibition of JNK1 by the scaffolding protein JIP1 and SP600125
Authors: Heo, Y.-S. / Kim, S.K. / Seo, C.I. / Kim, Y.K. / Sung, B.-J. / Lee, H.S. / Lee, J.I. / Park, S.-Y. / Kim, J.H. / Hwang, K.Y. / Hyun, Y.-L. / Jeon, Y.H. / Ro, S. / Cho, J.M. / Lee, T.G. / Yang, C.-H.
History
DepositionAug 23, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 8 isoform 4
B: 11-mer peptide from C-jun-amino-terminal kinase interacting protein 1


Theoretical massNumber of molelcules
Total (without water)43,9342
Polymers43,9342
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-7 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.398, 80.841, 83.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase 8 isoform 4 / JNK1


Mass: 42588.191 Da / Num. of mol.: 1 / Fragment: residues 1-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21B / Production host: Escherichia coli (E. coli) / References: UniProt: P45983, EC: 2.7.1.37
#2: Protein/peptide 11-mer peptide from C-jun-amino-terminal kinase interacting protein 1 / JIP1


Mass: 1345.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs peptide synthesis / References: UniProt: Q9WVI9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.73 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3000, 0.1M SODIUM CITRATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 11, 2003
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 18476 / Num. obs: 16980 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.1 Å2
Reflection shellResolution: 2.35→2.43 Å / % possible all: 72.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.82 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 479481.89 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 818 4.9 %RANDOM
Rwork0.226 ---
all0.229 18476 --
obs0.226 16729 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.7705 Å2 / ksol: 0.343461 e/Å3
Displacement parametersBiso mean: 61.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.77 Å20 Å20 Å2
2--0.89 Å20 Å2
3----7.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.35→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 0 95 2768
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 111 4.8 %
Rwork0.376 2203 -
obs--77.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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