+Open data
-Basic information
Entry | Database: PDB / ID: 3wdz | ||||||
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Title | Crystal Structure of Keap1 in Complex with phosphorylated p62 | ||||||
Components |
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Keywords | TRANSCRIPTION / Kelch repeat / p62 / Nucleus | ||||||
Function / homology | Function and homology information Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / response to mitochondrial depolarisation ...Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / response to mitochondrial depolarisation / aggrephagy / cellular response to carbohydrate stimulus / amphisome / negative regulation of toll-like receptor 4 signaling pathway / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / pexophagy / regulation of protein complex stability / endosome organization / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / non-membrane-bounded organelle assembly / Ub-specific processing proteases / phagophore assembly site / aggresome / regulation of canonical NF-kappaB signal transduction / negative regulation of response to oxidative stress / ubiquitin-modified protein reader activity / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / temperature homeostasis / Cul3-RING ubiquitin ligase complex / immune system process / mitophagy / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / autophagosome / cellular response to interleukin-4 / positive regulation of autophagy / energy homeostasis / signaling adaptor activity / inclusion body / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / sarcomere / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / regulation of autophagy / positive regulation of long-term synaptic potentiation / response to ischemia / actin filament / macroautophagy / protein kinase C binding / positive regulation of protein localization to plasma membrane / transcription coregulator activity / adherens junction / ionotropic glutamate receptor binding / P-body / protein catabolic process / PML body / autophagy / protein import into nucleus / disordered domain specific binding / late endosome / protein-macromolecule adaptor activity / signaling receptor activity / midbody / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / protein ubiquitination / positive regulation of protein phosphorylation / negative regulation of gene expression / focal adhesion / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Fukutomi, T. / Takagi, K. / Mizushima, T. / Tanaka, K. / Komatsu, M. / Yamamoto, M. | ||||||
Citation | Journal: Mol.Cell / Year: 2013 Title: Phosphorylation of p62 activates the Keap1-Nrf2 pathway during selective autophagy. Authors: Ichimura, Y. / Waguri, S. / Sou, Y.S. / Kageyama, S. / Hasegawa, J. / Ishimura, R. / Saito, T. / Yang, Y. / Kouno, T. / Fukutomi, T. / Hoshii, T. / Hirao, A. / Takagi, K. / Mizushima, T. / ...Authors: Ichimura, Y. / Waguri, S. / Sou, Y.S. / Kageyama, S. / Hasegawa, J. / Ishimura, R. / Saito, T. / Yang, Y. / Kouno, T. / Fukutomi, T. / Hoshii, T. / Hirao, A. / Takagi, K. / Mizushima, T. / Motohashi, H. / Lee, M.S. / Yoshimori, T. / Tanaka, K. / Yamamoto, M. / Komatsu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wdz.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wdz.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 3wdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wdz_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 3wdz_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 3wdz_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 3wdz_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/3wdz ftp://data.pdbj.org/pub/pdb/validation_reports/wd/3wdz | HTTPS FTP |
-Related structure data
Related structure data | 1x2jS 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: 34270.109 Da / Num. of mol.: 1 / Fragment: Keap1-DC, UNP residues 321-609 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1, Inrf2, Kiaa0132 / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21-Gold(DE3) / References: UniProt: Q9Z2X8 |
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#2: Protein/peptide | Mass: 1611.620 Da / Num. of mol.: 1 Fragment: Keap1 Interacting Region (KIR), UNP residues 346-359 Source method: obtained synthetically / Details: Mouse / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q64337 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.09 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 100mM Tris-HCl (pH 8.8), 0.2M Sodium Nitrate, 20% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 11646 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 6.51 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X2J Resolution: 2.6→42.67 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.195 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.224 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→42.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.604→2.672 Å / Total num. of bins used: 20
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