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- PDB-3o2m: Crystal Structure of JNK1-alpha1 isoform complex with a biaryl te... -

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Basic information

Entry
Database: PDB / ID: 3o2m
TitleCrystal Structure of JNK1-alpha1 isoform complex with a biaryl tetrazol (A-82118)
Components
  • C-Jun-amino-terminal kinase-interacting protein 1, JIP1, 10MER PEPTIDE
  • Mitogen-activated protein kinase 8
KeywordsTRANSFERASE/INHIBITOR / Serine Threonine Protein Kinase / ATP binding / Phosphorylation / Kinase-Inhibitor complex / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cell killing / dentate gyrus mossy fiber / JUN phosphorylation / regulation of DNA replication origin binding / 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 / JUN kinase activity ...positive regulation of cell killing / dentate gyrus mossy fiber / JUN phosphorylation / regulation of DNA replication origin binding / 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 / 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 / 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 / positive regulation of NLRP3 inflammasome complex assembly / DSCAM interactions / NRAGE signals death through JNK / Activation of the AP-1 family of transcription factors / dendritic growth cone / Fc-epsilon receptor signaling pathway / kinesin binding / regulation of JNK cascade / regulation of macroautophagy / mitogen-activated protein kinase / negative regulation of intrinsic apoptotic signaling pathway / stress-activated MAPK cascade / axonal growth cone / 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 / protein phosphatase binding / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / response to oxidative stress / neuron projection / positive regulation of apoptotic process / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / neuronal cell body / synapse / endoplasmic reticulum membrane / positive regulation of gene expression / regulation of DNA-templated transcription / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / signal transduction / nucleoplasm / ATP binding / membrane / identical protein 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-46A / Mitogen-activated protein kinase 8 / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAbad-Zapatero, C.
CitationJournal: Acs Chem.Biol. / Year: 2011
Title: Discovery and characterization of non-ATP site inhibitors of the mitogen activated protein (MAP) kinases.
Authors: Comess, K.M. / Sun, C. / Abad-Zapatero, C. / Goedken, E.R. / Gum, R.J. / Borhani, D.W. / Argiriadi, M. / Groebe, D.R. / Jia, Y. / Clampit, J.E. / Haasch, D.L. / Smith, H.T. / Wang, S. / ...Authors: Comess, K.M. / Sun, C. / Abad-Zapatero, C. / Goedken, E.R. / Gum, R.J. / Borhani, D.W. / Argiriadi, M. / Groebe, D.R. / Jia, Y. / Clampit, J.E. / Haasch, D.L. / Smith, H.T. / Wang, S. / Song, D. / Coen, M.L. / Cloutier, T.E. / Tang, H. / Cheng, X. / Quinn, C. / Liu, B. / Xin, Z. / Liu, G. / Fry, E.H. / Stoll, V. / Ng, T.I. / Banach, D. / Marcotte, D. / Burns, D.J. / Calderwood, D.J. / Hajduk, P.J.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 8
F: C-Jun-amino-terminal kinase-interacting protein 1, JIP1, 10MER PEPTIDE
B: Mitogen-activated protein kinase 8
G: C-Jun-amino-terminal kinase-interacting protein 1, JIP1, 10MER PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,33710
Polymers88,1264
Non-polymers1,2116
Water0
1
A: Mitogen-activated protein kinase 8
F: C-Jun-amino-terminal kinase-interacting protein 1, JIP1, 10MER PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6695
Polymers44,0632
Non-polymers6063
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-40 kcal/mol
Surface area16980 Å2
MethodPISA
2
B: Mitogen-activated protein kinase 8
G: C-Jun-amino-terminal kinase-interacting protein 1, JIP1, 10MER PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6695
Polymers44,0632
Non-polymers6063
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-40 kcal/mol
Surface area17000 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-101 kcal/mol
Surface area32110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.379, 158.379, 123.959
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTwo undecapeptides in one asymmetric unit

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Components

#1: Protein Mitogen-activated protein kinase 8 / MAP kinase 8 / MAPK 8 / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1 / JNK-46 / ...MAP kinase 8 / MAPK 8 / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1 / JNK-46 / Stress-activated protein kinase 1


Mass: 42874.523 Da / Num. of mol.: 2 / Fragment: unp residues 1-364 / Mutation: T183E, Y185E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JNK1, MAPK8, PRKM8, SAPK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P45983, mitogen-activated protein kinase
#2: Protein/peptide C-Jun-amino-terminal kinase-interacting protein 1, JIP1, 10MER PEPTIDE / JNK-interacting protein 1 / JIP-1 / JNK MAP kinase scaffold protein 1


Mass: 1188.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9WVI9
#3: Chemical ChemComp-46A / N-butyl-4,6-dimethyl-N-{[2'-(2H-tetrazol-5-yl)biphenyl-4-yl]methyl}pyrimidin-2-amine


Mass: 413.518 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27N7
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
Sequence detailsAUTHORS SEQUENCE MATCHES WITH SEQUENCE PUBLISHED BY HEO ET AL. (2004) EMBO JOURNAL VOL. 23, 2185- ...AUTHORS SEQUENCE MATCHES WITH SEQUENCE PUBLISHED BY HEO ET AL. (2004) EMBO JOURNAL VOL. 23, 2185-2195 AND SUPPLEMENTAL INFORMATION

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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: 5.28 Å3/Da / Density % sol: 76.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Hanging drop : 2 ul of 10 mg/ml protein plus 2 ul of well solution Well solution : 3.0 M ammonium sulfate, 10 % glycerol Co-crystallization : compounds in DMSO added to the protein solution ...Details: Hanging drop : 2 ul of 10 mg/ml protein plus 2 ul of well solution Well solution : 3.0 M ammonium sulfate, 10 % glycerol Co-crystallization : compounds in DMSO added to the protein solution (0.62 mM compound with protein concentration of 9 mg/ml) more than 1 hour incubation on ice, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 49440 / Num. obs: 46583 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 49.7 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.88 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 389580.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.266 4384 10 %RANDOM
Rwork0.233 ---
obs0.233 43787 88.5 %-
all-49477 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.5612 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-20 Å
Luzzati sigma a0.42 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5955 0 82 0 6037
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d1.02
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 545 9.7 %
Rwork0.317 5078 -
obs--69 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramso4.top
X-RAY DIFFRACTION3ion.paramlig.top
X-RAY DIFFRACTION4so4.par
X-RAY DIFFRACTION5lig.par

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