|Entry||Database: PDB / ID: 2kkc|
|Title||NMR structure of the p62 PB1 domain|
|Keywords||SIGNALING PROTEIN / TRANSPORT PROTEIN / p62 / PB1 / autophagy / ubiquitin-proteasome system / NF-kB signaling / Alternative splicing / Apoptosis / Cytoplasm / Differentiation / Endosome / Immune response / Metal-binding / Nucleus / Phosphoprotein / Zinc / Zinc-finger|
|Function / homology|
Function and homology information
protein localization to perinuclear region of cytoplasm / amphisome / selective autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / regulation of protein complex stability / endosome organization / mitophagy / phagophore assembly site ...protein localization to perinuclear region of cytoplasm / amphisome / selective autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / regulation of protein complex stability / endosome organization / mitophagy / phagophore assembly site / K63-linked polyubiquitin modification-dependent protein binding / autolysosome / immune system process / aggresome / sperm midpiece / regulation of I-kappaB kinase/NF-kappaB signaling / ionotropic glutamate receptor binding / autophagosome / sarcomere / inclusion body / response to ischemia / negative regulation of protein ubiquitination / mitochondrion organization / SH2 domain binding / ubiquitin binding / protein kinase C binding / P-body / positive regulation of long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / macroautophagy / PML body / autophagy / late endosome / cell differentiation / positive regulation of protein phosphorylation / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / enzyme binding / mitochondrion / zinc ion binding / identical protein binding / cytosol / cytoplasm
Zinc finger, ZZ-type / PB1 domain / UBA-like superfamily / Ubiquitin-associated domain / Sequestosome-1, UBA domain / PB1 domain / Zinc finger, ZZ-type superfamily / Sequestosome-1, PB1 domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...Zinc finger, ZZ-type / PB1 domain / UBA-like superfamily / Ubiquitin-associated domain / Sequestosome-1, UBA domain / PB1 domain / Zinc finger, ZZ-type superfamily / Sequestosome-1, PB1 domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
|Biological species||Rattus norvegicus (Norway rat)|
|Method||SOLUTION NMR / torsion angle dynamics, simulated annealing|
|Model details||lowest energy, model 1|
|Authors||Yokochi, M. / Inagaki, F.|
|Citation||Journal: J.Biomol.Nmr / Year: 2009|
Title: The NMR structure of the p62 PB1 domain, a key protein in autophagy and NF-kappaB signaling pathway
Authors: Saio, T. / Yokochi, M. / Inagaki, F.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
|#1: Protein|| |
Mass: 11428.100 Da / Num. of mol.: 1 / Fragment: PB1 domain, OPR domain, residues 3-100 / Mutation: D67A, D69R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O08623
|Experiment||Method: SOLUTION NMR|
|Details||Contents: 1mM [U-99% 13C; U-99% 15N] p62 PB1-1, 90% H2O/10% D2O|
Solvent system: 90% H2O/10% D2O
|Sample||Conc.: 1 mM / Component: p62 PB1-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]|
|Sample conditions||Ionic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K|
|NMR spectrometer||Type: Varian Unity Inova / Manufacturer: Varian / Model: Unity Inova / Field strength: 800 MHz|
|Refinement||Method: torsion angle dynamics, simulated annealing / Software ordinal: 1|
|NMR representative||Selection criteria: lowest energy|
|NMR ensemble||Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1|
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