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 / autophagy of mitochondrion ...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 / autophagy of mitochondrion / pexophagy / regulation of protein complex stability / endosome organization / non-membrane-bounded organelle assembly / molecular sequestering activity / ubiquitin-modified protein reader activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / negative regulation of ferroptosis / autolysosome / endosomal transport / intracellular non-membrane-bounded organelle / temperature homeostasis / immune system process / K63-linked polyubiquitin modification-dependent protein binding / mitophagy / autophagosome / positive regulation of autophagy / signaling adaptor activity / energy homeostasis / inclusion body / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / ionotropic glutamate receptor binding / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / sarcomere / positive regulation of protein localization to plasma membrane / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / macroautophagy / protein kinase C binding / P-body / protein catabolic process / PML body / receptor tyrosine kinase binding / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / protein localization / Signaling by ALK fusions and activated point mutants / late endosome / signaling receptor activity / Neddylation / protein-macromolecule adaptor 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 / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / apoptotic process / 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
Ubiquitin-bindingproteinp62 / Sequestosome-1 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / EBI3- ...Sequestosome-1 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / EBI3-associated protein of 60 kDa / p60 / EBIAP
Mass: 5744.406 Da / Num. of mol.: 1 / Fragment: UBA domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-15N HSQC
1
2
1
3D 1H-15N TOCSY
1
3
1
3D 1H-15N NOESY
1
4
2
2D 1H-13C HSQC
1
5
2
3D HN(CA)CB
1
6
2
3DCBCA(CO)NH
1
7
2
3D (H)CCH-TOCSY
1
8
2
3D 1H-13C NOESY
1
9
2
3D HNCO
1
10
2
3DHN(CA)CO
1
11
3
2D 1H-15N HSQC-IPAP
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1 mM [U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide, 90% H2O/10% D2O
90% H2O/10% D2O
2
1 mM [U-100% 13C; U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide, 90% H2O/10% D2O
90% H2O/10% D2O
3
1 mM [U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide, 90% H2O/10% D2O
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
1mM
entity
[U-100% 15N]
1
50mM
potassiumphosphate
1
50mM
sodiumchloride
1
0.04 %
sodiumazide
1
1mM
entity
[U-100% 13C; U-100% 15N]
2
50mM
potassiumphosphate
2
50mM
sodiumchloride
2
0.04 %
sodiumazide
2
1mM
entity
[U-100% 15N]
3
50mM
potassiumphosphate
3
50mM
sodiumchloride
3
0.04 %
sodiumazide
3
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
-
Processing
NMR software
Name
Version
Developer
Classification
X-PLOR NIH
2.14
Schwieters, Kuszewski, TjandraandClore
structuresolution
XwinNMR
3.5
BrukerBiospin
collection
XwinNMR
3.5
BrukerBiospin
processing
CcpNMR
1.0.10
CCPN
peakpicking
CcpNMR
1.0.10
CCPN
dataanalysis
CcpNMR
1.0.10
CCPN
chemicalshiftassignment
TALOS
Cornilescu, DelaglioandBax
geometryoptimization
X-PLOR NIH
2.14
Schwieters, Kuszewski, TjandraandClore
refinement
Refinement
Method: simulated annealing / Software ordinal: 1 Details: In the first stage, high temperature Cartesian dynamics was performed at 1000 K with a time step of 0.005 ps, for 20,000 steps, using the Verlet integrator. During the second cooling phase ...Details: In the first stage, high temperature Cartesian dynamics was performed at 1000 K with a time step of 0.005 ps, for 20,000 steps, using the Verlet integrator. During the second cooling phase of the protocol, the temperature was reduced from 1000 K to 100 K in steps of 50 K, with a time step of 5 fs, over 40,000 steps during which the relative weighting of non-bonded energy terms were increased from 10% of their default values to their force field default. These initial structures were then refined with another 10000 cooling step
NMR constraints
NOE constraints total: 886 / NOE intraresidue total count: 341 / NOE long range total count: 85 / NOE medium range total count: 184 / NOE sequential total count: 204 / Protein phi angle constraints total count: 31 / Protein psi angle constraints total count: 31
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 21
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