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- PDB-3vul: Crystal structure of a cysteine-deficient mutant M1 in MAP kinase JNK1 -

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Basic information

Entry
Database: PDB / ID: 3vul
TitleCrystal structure of a cysteine-deficient mutant M1 in MAP kinase JNK1
Components
  • Mitogen-activated protein kinase 8
  • Peptide from C-Jun-amino-terminal kinase-interacting protein 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSCRIPTION / phosphorylation / ATP Binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / JUN phosphorylation / positive regulation of cell killing / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / basal dendrite / positive regulation of establishment of protein localization to mitochondrion / Activation of BIM and translocation to mitochondria / negative regulation of JUN kinase activity ...dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / JUN phosphorylation / positive regulation of cell killing / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / basal dendrite / positive regulation of establishment of protein localization to mitochondrion / Activation of BIM and translocation to mitochondria / negative regulation of JUN kinase activity / WNT5:FZD7-mediated leishmania damping / MAP-kinase scaffold activity / JUN kinase binding / regulation of JNK cascade / positive regulation of cyclase activity / histone deacetylase regulator activity / cellular response to stress / NRAGE signals death through JNK / positive regulation of NLRP3 inflammasome complex assembly / protein kinase inhibitor activity / Activation of the AP-1 family of transcription factors / negative regulation of intrinsic apoptotic signaling pathway / Fc-epsilon receptor signaling pathway / kinesin binding / regulation of macroautophagy / mitogen-activated protein kinase / JUN kinase activity / response to UV / protein serine/threonine kinase binding / response to mechanical stimulus / stress-activated MAPK cascade / energy homeostasis / vesicle-mediated transport / JNK cascade / positive regulation of protein metabolic process / negative regulation of protein binding / NRIF signals cell death from the nucleus / cellular response to amino acid starvation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / cellular response to reactive oxygen species / peptidyl-threonine phosphorylation / positive regulation of JNK cascade / FCERI mediated MAPK activation / mitochondrial membrane / regulation of circadian rhythm / cellular response to mechanical stimulus / histone deacetylase binding / cellular senescence / Signaling by ALK fusions and activated point mutants / rhythmic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to lipopolysaccharide / peptidyl-serine phosphorylation / cellular response to oxidative stress / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / protein phosphorylation / positive regulation of apoptotic process / axon / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / synapse / positive regulation of gene expression / endoplasmic reticulum membrane / regulation of DNA-templated transcription / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / nucleoplasm / ATP binding / 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 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
Stress-activated protein kinase JNK / 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: 2.81 Å
AuthorsNakaniwa, T. / Kinoshita, T. / Inoue, T.
CitationJournal: Biochemistry / Year: 2012
Title: Seven cysteine-deficient mutants depict the interplay between thermal and chemical stabilities of individual cysteine residues in mitogen-activated protein kinase c-Jun N-terminal kinase 1
Authors: Nakaniwa, T. / Fukada, H. / Inoue, T. / Gouda, M. / Nakai, R. / Kirii, Y. / Adachi, M. / Tamada, T. / Segawa, S. / Kuroki, R. / Tada, T. / Kinoshita, T.
History
DepositionJul 2, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 8
F: Peptide from C-Jun-amino-terminal kinase-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)43,9872
Polymers43,9872
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-7 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.781, 161.781, 87.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

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Components

#1: Protein Mitogen-activated protein kinase 8 / Mitogen-activated protein kinase 8 isoform JNK1 beta2 / Mitogen-activated protein kinase 8 / ...Mitogen-activated protein kinase 8 isoform JNK1 beta2 / Mitogen-activated protein kinase 8 / isoform CRA_d / cDNA FLJ77387 / highly similar to Homo sapiens mitogen-activated protein kinase 8 (MAPK8) / transcript variant 4 / mRNA


Mass: 42641.078 Da / Num. of mol.: 1 / Fragment: kinase domain, UNP residues 1-364 / Mutation: C245S, C116S, C163A, C79V, C137V, C213V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A1L4K2, UniProt: P45983*PLUS, mitogen-activated protein kinase
#2: Protein/peptide Peptide from C-Jun-amino-terminal kinase-interacting protein 1 / JIP-1 / JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / ...JIP-1 / JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / Mitogen-activated protein kinase 8-interacting protein 1


Mass: 1345.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQF2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.2M ammonium sulfate, 0.2M sodium chloride, 0.1M sodium cacodylate pH 6.5 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A
DetectorType: ADSC QUANTUM 270 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16976 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→33.78 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.858 / SU B: 15.437 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R: 0.582 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31501 853 5.1 %RANDOM
Rwork0.24866 ---
obs0.25207 15954 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.439 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.81→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 0 37 2896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222922
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9713953
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2965351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.82424.519135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.85215534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5821516
X-RAY DIFFRACTIONr_chiral_restr0.1330.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212184
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_it1.0191.51771
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93422876
X-RAY DIFFRACTIONr_scbond_it2.21731151
X-RAY DIFFRACTIONr_scangle_it3.8574.51077
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.805→2.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 64 -
Rwork0.309 1124 -
obs--97.22 %

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