+Open data
-Basic information
Entry | Database: PDB / ID: 4ux9 | ||||||
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Title | Crystal structure of JNK1 bound to a MKK7 docking motif | ||||||
Components |
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Keywords | TRANSFERASE / JNK1 / INTRINSICALLY DISORDERED DOMAINS / MKK7 | ||||||
Function / homology | Function and homology information positive regulation of cell killing / JUN phosphorylation / regulation of DNA replication origin binding / : / JUN kinase kinase activity / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / regulation of motor neuron apoptotic process / Activation of BIM and translocation to mitochondria ...positive regulation of cell killing / JUN phosphorylation / regulation of DNA replication origin binding / : / JUN kinase kinase activity / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / regulation of motor neuron apoptotic process / Activation of BIM and translocation to mitochondria / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / mitogen-activated protein kinase kinase / protein serine/threonine kinase binding / positive regulation of cyclase activity / histone deacetylase regulator activity / response to osmotic stress / positive regulation of NLRP3 inflammasome complex assembly / DSCAM interactions / NRAGE signals death through JNK / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / regulation of macroautophagy / mitogen-activated protein kinase / cellular response to interleukin-1 / response to tumor necrosis factor / stress-activated MAPK cascade / response to mechanical stimulus / response to UV / positive regulation of JUN kinase activity / JNK cascade / positive regulation of telomerase activity / cellular response to cadmium ion / positive regulation of telomere maintenance via telomerase / 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 / molecular function activator activity / FCERI mediated MAPK activation / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / regulation of circadian rhythm / cellular response to reactive oxygen species / response to wounding / 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 / response to heat / protein phosphatase binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / response to oxidative stress / cellular response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / positive regulation of apoptotic process / axon / phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / apoptotic process / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / enzyme binding / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Kragelj, J. / Palencia, A. / Nanao, M.H. / Maurin, D. / Bouvignies, G. / Blackledge, M. / Ringkjobing-Jensen, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structure and Dynamics of the Mkk7-Jnk Signaling Complex. Authors: Kragelj, J. / Palencia, A. / Nanao, M.H. / Maurin, D. / Bouvignies, G. / Blackledge, M. / Jensen, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ux9.cif.gz | 294.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ux9.ent.gz | 240.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ux9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/4ux9 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/4ux9 | HTTPS FTP |
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-Related structure data
Related structure data | 2xrwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 42096.742 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P45983, mitogen-activated protein kinase #2: Protein/peptide | Mass: 1391.660 Da / Num. of mol.: 4 / Fragment: RESIDUES 37-48 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O14733 #3: Chemical | ChemComp-ANP / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % / Description: NONE |
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Crystal grow | Details: 50 MM HEPES 150 MM NACL 2 MM MGSO4 1 MM TCEP 2.6 M NH4SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2014 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→50 Å / Num. obs: 75436 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 66.09 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.66 |
Reflection shell | Resolution: 2.34→2.42 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.66 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XRW Resolution: 2.34→49.21 Å / Cor.coef. Fo:Fc: 0.9473 / Cor.coef. Fo:Fc free: 0.9308 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.285 / SU Rfree Blow DPI: 0.216 / SU Rfree Cruickshank DPI: 0.222
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Displacement parameters | Biso mean: 66.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.329 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→49.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.34→2.4 Å / Total num. of bins used: 20
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