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- PDB-4izy: Crystal structure of JNK1 in complex with JIP1 peptide and 4-{4-[... -

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Basic information

Entry
Database: PDB / ID: 4izy
TitleCrystal structure of JNK1 in complex with JIP1 peptide and 4-{4-[4-(4-Methanesulfonyl-piperidin-1-yl)-indol-1-yl]-pyrimidin-2-ylamino}-cyclohexan
Components
  • C-Jun-amino-terminal kinase-interacting protein 1
  • Mitogen-activated protein kinase 8
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


cellular response to stress / positive regulation of cell killing / dentate gyrus mossy fiber / JUN phosphorylation / regulation of CD8-positive, alpha-beta T cell proliferation / regulation of DNA replication origin binding / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria ...cellular response to stress / positive regulation of cell killing / dentate gyrus mossy fiber / JUN phosphorylation / regulation of CD8-positive, alpha-beta T cell proliferation / regulation of DNA replication origin binding / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / protein serine/threonine kinase binding / JUN kinase binding / positive regulation of cyclase activity / histone deacetylase regulator activity / positive regulation of NLRP3 inflammasome complex assembly / DSCAM interactions / NRAGE signals death through JNK / protein kinase inhibitor activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / kinesin binding / regulation of JNK cascade / MAP kinase activity / regulation of macroautophagy / mitogen-activated protein kinase / negative regulation of intrinsic apoptotic signaling pathway / stress-activated MAPK cascade / response to mechanical stimulus / response to UV / JNK cascade / vesicle-mediated transport / cellular response to cadmium ion / cellular response to amino acid starvation / positive regulation of protein metabolic process / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of protein binding / mitochondrial membrane / FCERI mediated MAPK activation / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / regulation of circadian rhythm / cellular response to reactive oxygen species / cellular response to mechanical stimulus / histone deacetylase binding / rhythmic process / regulation of protein localization / cellular senescence / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to oxidative stress / peptidyl-serine phosphorylation / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / cellular response to lipopolysaccharide / positive regulation of apoptotic process / axon / phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / synapse / endoplasmic reticulum membrane / positive regulation of gene expression / 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 / 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-1J2 / 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 / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsKuglstatter, A. / Shao, A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Development of indole/indazole-aminopyrimidines as inhibitors of c-Jun N-terminal kinase (JNK): optimization for JNK potency and physicochemical properties.
Authors: Gong, L. / Han, X. / Silva, T. / Tan, Y.C. / Goyal, B. / Tivitmahaisoon, P. / Trejo, A. / Palmer, W. / Hogg, H. / Jahagir, A. / Alam, M. / Wagner, P. / Stein, K. / Filonova, L. / Loe, B. / ...Authors: Gong, L. / Han, X. / Silva, T. / Tan, Y.C. / Goyal, B. / Tivitmahaisoon, P. / Trejo, A. / Palmer, W. / Hogg, H. / Jahagir, A. / Alam, M. / Wagner, P. / Stein, K. / Filonova, L. / Loe, B. / Makra, F. / Rotstein, D. / Rapatova, L. / Dunn, J. / Zuo, F. / Dal Porto, J. / Wong, B. / Jin, S. / Chang, A. / Tran, P. / Hsieh, G. / Niu, L. / Shao, A. / Reuter, D. / Hermann, J. / Kuglstatter, A. / Goldstein, D.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 8
B: C-Jun-amino-terminal kinase-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4033
Polymers43,9342
Non-polymers4701
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-8 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.426, 82.371, 82.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsOne biological assembly in asymmetric unit.

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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: 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) / Gene: MAPK8, hCG_23734 / Production host: Escherichia coli (E. coli)
References: UniProt: A1L4K2, UniProt: P45983*PLUS, EC: 2.7.1.37
#2: Protein/peptide 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 / Fragment: RESIDUES 157-167 / Source method: obtained synthetically / Details: Chemical synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQF2
#3: Chemical ChemComp-1J2 / trans-4-[(4-{4-[4-(methylsulfonyl)piperidin-1-yl]-1H-indol-1-yl}pyrimidin-2-yl)amino]cyclohexanol


Mass: 469.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H31N5O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 3350, 0.2 M LiSO4, 0.1 M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→48.74 Å / Num. obs: 17753 / % possible obs: 99.63 % / Redundancy: 5.2 % / Biso Wilson estimate: 52.8 Å2 / Rsym value: 0.083 / Net I/σ(I): 17.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1268 / Rsym value: 0.763 / % possible all: 98.39

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1UKH

1ukh


Resolution: 2.3→48.74 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.923 / SU B: 15.608 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26115 962 5.1 %RANDOM
Rwork0.23758 ---
obs0.2388 17753 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 33 77 2784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222773
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.993752
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2935326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44124.309123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04415504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8131515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212063
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_it0.531.51656
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02222690
X-RAY DIFFRACTIONr_scbond_it1.45531117
X-RAY DIFFRACTIONr_scangle_it2.5114.51062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 73 -
Rwork0.315 1268 -
obs--98.39 %
Refinement TLS params.Method: refined / Origin x: -9.1176 Å / Origin y: 0.1061 Å / Origin z: -12.4725 Å
111213212223313233
T0.0082 Å2-0.0024 Å20.0251 Å2-0.0104 Å20.0009 Å2--0.088 Å2
L0.4873 °2-0.1333 °20.3221 °2-0.2823 °2-0.0896 °2--0.2145 °2
S-0.0098 Å °0.0014 Å °0.0151 Å °0.0043 Å °0.0128 Å °0.0011 Å °-0.0083 Å °-0.0007 Å °-0.003 Å °

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