- PDB-2ktr: NMR structure of p62 PB1 dimer determined based on PCS -
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Basic information
Entry
Database: PDB / ID: 2ktr
Title
NMR structure of p62 PB1 dimer determined based on PCS
Components
(Sequestosome-1) x 2
Keywords
Signaling Protein / Transport Protein / Autophagy / NF-kB signaling / homo-oligomer / PB1 dimer
Function / homology
Function and homology information
Interleukin-1 signaling / Pexophagy / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / p75NTR recruits signalling complexes / KEAP1-NFE2L2 pathway / PINK1-PRKN Mediated Mitophagy / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy ...Interleukin-1 signaling / Pexophagy / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / p75NTR recruits signalling complexes / KEAP1-NFE2L2 pathway / PINK1-PRKN Mediated Mitophagy / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / Lewy body / aggrephagy / response to mitochondrial depolarisation / amphisome / pexophagy / endosome organization / regulation of protein complex stability / phagophore assembly site / : / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / autolysosome / temperature homeostasis / immune system process / mitophagy / autophagosome / positive regulation of autophagy / energy homeostasis / inclusion body / signaling adaptor activity / sperm midpiece / ionotropic glutamate receptor binding / sarcomere / negative regulation of protein ubiquitination / ubiquitin binding / SH2 domain binding / positive regulation of long-term synaptic potentiation / response to ischemia / P-body / protein kinase C binding / positive regulation of protein localization to plasma membrane / macroautophagy / protein catabolic process / PML body / autophagy / cellular response to reactive oxygen species / protein import into nucleus / protein-macromolecule adaptor activity / late endosome / signaling receptor activity / transcription by RNA polymerase II / cell differentiation / positive regulation of protein phosphorylation / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / zinc ion binding / identical protein binding / cytosol / cytoplasm Similarity search - Function
Mass: 158.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tb
Compound details
A67, R69, E207, AND A294 ARE MUTATIONS FOR THE PREVENTION OF HOMO-OLIGOMERIZATION. S42, S226, AND ...A67, R69, E207, AND A294 ARE MUTATIONS FOR THE PREVENTION OF HOMO-OLIGOMERIZATION. S42, S226, AND S242 ARE FOR THE FIXATION OF LANTHANIDE-BINDING PEPTIDE TAG(LBT).
Sequence details
THE SEQUENCE CYVDTNNDGAYEGDELHMG OF CHAIN A IS FOR LANTHANIDE-BINDING PEPTIDE SEQUENCE.
Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 Details: In this work, the dimer structure of p62 PB1 was determined by using a rigid-body docking calculation based on the pseudo-contact shift. In the docking calculation, the coordinates of chain ...Details: In this work, the dimer structure of p62 PB1 was determined by using a rigid-body docking calculation based on the pseudo-contact shift. In the docking calculation, the coordinates of chain A were held fixed, whereas the coordinates of chain B were treated as a rigid body and set free to rotate and translate. The differences among the models are relative orientations between chain A and chain B, not each coordinates. In the calculation, monomer structures of DR and KE were docked each other based on the inter-subunit restraints from pseudo-contact shifts. The coordinates of DR and KE were generated from the monomer structure of DR (2kkc), using PyMOL software. For pseudo-contact shift restraints, we need a paramagnetic lanthanide ion fixed in the target protein. To fix a lanthanide ions to DR, we utilized the lanthanide binding peptide tag (LBT).The chain A represents LBT-DR, and chain B does KE. We collected the pseudo-contact shift restrains using LBT-DR/KE complex, while the docking calculations were performed using the coordinates without LBT.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1
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