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Yorodumi- PDB-2xrw: Linear binding motifs for JNK and for calcineurin antagonisticall... -
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-Basic information
Entry | Database: PDB / ID: 2xrw | ||||||
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Title | Linear binding motifs for JNK and for calcineurin antagonistically control the nuclear shuttling of NFAT4 | ||||||
Components |
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Keywords | TRANSCRIPTION / MAPK SIGNALING PATHWAYS / LINEAR BINDING MOTIF | ||||||
Function / homology | Function and homology information positive regulation of artery morphogenesis / positive regulation of cell killing / JUN phosphorylation / regulation of DNA replication origin binding / Interleukin-38 signaling / negative regulation of vascular associated smooth muscle cell differentiation / Activation of BMF and translocation to mitochondria / cellular response to stress / basal dendrite / Activation of BIM and translocation to mitochondria ...positive regulation of artery morphogenesis / positive regulation of cell killing / JUN phosphorylation / regulation of DNA replication origin binding / Interleukin-38 signaling / negative regulation of vascular associated smooth muscle cell differentiation / Activation of BMF and translocation to mitochondria / cellular response to stress / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / DN4 thymocyte differentiation / calcineurin-NFAT signaling cascade / WNT5:FZD7-mediated leishmania damping / positive thymic T cell selection / positive regulation of cyclase activity / histone deacetylase regulator activity / positive regulation of NLRP3 inflammasome complex assembly / DSCAM interactions / CLEC7A (Dectin-1) induces NFAT activation / protein serine/threonine kinase binding / NRAGE signals death through JNK / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / Calcineurin activates NFAT / regulation of macroautophagy / mitogen-activated protein kinase / stress-activated MAPK cascade / response to mechanical stimulus / response to UV / JNK cascade / cellular response to cadmium ion / cellular response to amino acid starvation / positive regulation of protein metabolic process / NRIF signals cell death from the nucleus / FCERI mediated Ca+2 mobilization / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of miRNA transcription / negative regulation of protein binding / FCERI mediated MAPK activation / peptidyl-threonine phosphorylation / regulation of circadian rhythm / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to reactive oxygen species / histone deacetylase binding / cellular response to mechanical stimulus / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / cellular senescence / sequence-specific double-stranded DNA binding / rhythmic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / peptidyl-serine phosphorylation / protein phosphatase binding / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / response to oxidative stress / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / phosphorylation / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Barkai, T. / Toeoroe, I. / Garai, A. / Remenyi, A. | ||||||
Citation | Journal: Sci. Signal / Year: 2012 Title: Specificity of Linear Motifs that Bind to a Common Mitogen-Activated Protein Kinase Docking Groove. Authors: Garai, A. / Zeke, A. / Gogl, G. / Toro, I. / Fordos, F. / Blankenburg, H. / Barkai, T. / Varga, J. / Alexa, A. / Emig, D. / Albrecht, M. / Remenyi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xrw.cif.gz | 173 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xrw.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xrw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/2xrw ftp://data.pdbj.org/pub/pdb/validation_reports/xr/2xrw | HTTPS FTP |
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-Related structure data
Related structure data | 2xs0C 2y8oC 2y9qC 3teiC 4fmqC 1ukhS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42774.355 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-364 Source method: isolated from a genetically manipulated source Details: LAST 20 RESIDUES TRUNCATED / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: A1L4K2, UniProt: P45983*PLUS, mitogen-activated protein kinase | ||||
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#2: Protein/peptide | Mass: 1740.977 Da / Num. of mol.: 1 / Fragment: FRAGMENT OF NFAT4, RESIDUES 141-154 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q12968 | ||||
#3: Chemical | ChemComp-ANP / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | AMPPNP (ANP): THE GAMMA-PHOSPHATE GROUP IS NOT MODELLED. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.59 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 18-20% PEG 8000, 100 MM SODIUM CITRATE PH 5.5, 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 18, 2010 / Details: TOROIDAL MIRRORS |
Radiation | Monochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→47.07 Å / Num. obs: 86996 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.45 |
Reflection shell | Resolution: 1.33→1.4 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.98 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UKH Resolution: 1.33→25.689 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 19.43 / Stereochemistry target values: ML Details: RESIDUES 0, 173-188, 366-370 IN CHAIN A, RESIDUES 141-142 IN CHAIN B ARE COMPLETELY DISORDERED. THE AMPPNP RESIDUE IS PARTIALLY DISORDERED.
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.457 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.33→25.689 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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