- PDB-2knv: NMR dimer structure of the UBA domain of p62 (SQSTM1) -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2knv
Title
NMR dimer structure of the UBA domain of p62 (SQSTM1)
Components
Sequestosome-1
Keywords
PROTEIN BINDING / Ubiquitin binding / Ubiquitin-Associated domain / Paget s disease of bone / helical bundle / dimer
Function / homology
Function and homology information
brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / pexophagy ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / pexophagy / regulation of protein complex stability / autophagy of mitochondrion / endosome organization / non-membrane-bounded organelle assembly / molecular sequestering activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / Nuclear events mediated by NFE2L2 / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / endosomal transport / temperature homeostasis / immune system process / mitophagy / autophagosome / positive regulation of autophagy / energy homeostasis / signaling adaptor activity / inclusion body / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / sarcomere / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / macroautophagy / protein kinase C binding / positive regulation of protein localization to plasma membrane / ionotropic glutamate receptor binding / P-body / protein catabolic process / protein localization / receptor tyrosine kinase binding / PML body / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / late endosome / protein-macromolecule adaptor activity / Neddylation / signaling receptor activity / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / intracellular membrane-bounded organelle / 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 / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol Similarity search - Function
Sequestosome-1 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62 ...Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62 / EBI3-associated protein of 60 kDa / p60 / EBIAP
Mass: 5744.406 Da / Num. of mol.: 2 / Fragment: UBA domain, UNP residues 387-436 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: Q13501
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR Details: Dimer structure of the p62 UBA domain solved using intermolecular NOEs
NMR experiment
Type: Half-filter NOESY
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Sample preparation
Details
Contents: 0.3 mM [U-99% 13C; U-99% 15N] UBA-1, 0.6 mM UBA-2, 50 mM potassium phosphate-3, 50 mM sodium chloride-4, 0.04 % sodium azide-5, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.3mM
UBA-1
[U-99% 13C; U-99% 15N]
1
0.6mM
UBA-2
1
50mM
potassium phosphate-3
1
50mM
sodium chloride-4
1
0.04 %
sodium azide-5
1
Sample conditions
pH: 7 / Pressure: ambient / Temperature: 298 K
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NMR measurement
NMR spectrometer
Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz
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Processing
NMR software
Name
Version
Developer
Classification
TopSpin
2.1
BrukerBiospin
collection
Ccpnmr
1.15
CCPN
dataanalysis
HADDOCK
2
AlexandreBonvin
structuresolution
HADDOCK
2
AlexandreBonvin
refinement
Refinement
Method: molecular dynamics / Software ordinal: 1
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1
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