3B0F | pdb_00003b0f

Crystal structure of the UBA domain of p62 and its interaction with ubiquitin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3b0fb_	All alpha proteins	RuvA C-terminal domain-like	UBA-like	UBA domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3b0fa_	All alpha proteins	RuvA C-terminal domain-like	UBA-like	UBA domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	UBA-like	8084768	3001235	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	UBA-like	8084768	3001235	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	UBA_5	e3b0fB1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UBA_5	ECOD (1.6)
A	UBA_5	e3b0fA1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UBA_5	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Sequestosome-1	protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding binding ubiquitin-modified protein reader activity ubiquitin-like protein reader activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding identical protein binding molecular transducer activity signaling receptor activity signaling adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding binding ubiquitin-modified protein reader activity ubiquitin-like protein reader activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding identical protein binding molecular transducer activity signaling receptor activity signaling adaptor activity transcription regulator activity transcription coregulator activity SH2 domain binding protein domain specific binding molecular condensate scaffold activity ubiquitin binding ubiquitin-like protein binding ionotropic glutamate receptor binding signaling receptor binding glutamate receptor binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding molecular sequestering activity protein sequestering activity kinase binding protein kinase C binding protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus pattern recognition receptor signaling pathway negative regulation of biological process regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus pattern recognition receptor signaling pathway negative regulation of biological process regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface toll-like receptor signaling pathway innate immune response-activating signaling pathway regulation of biological process immune response response to other organism immune response-activating cell surface receptor signaling pathway regulation of innate immune response response to external stimulus regulation of toll-like receptor 4 signaling pathway regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of signaling signaling positive regulation of biological process innate immune response activating cell surface receptor signaling pathway negative regulation of cell communication positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress negative regulation of cellular process innate immune response response to external biotic stimulus negative regulation of toll-like receptor 4 signaling pathway cell surface pattern recognition receptor signaling pathway regulation of signaling positive regulation of innate immune response cell surface receptor signaling pathway negative regulation of response to stimulus defense response biological regulation defense response to symbiont negative regulation of signal transduction negative regulation of immune system process immune system process toll-like receptor 4 signaling pathway regulation of cell communication cellular process negative regulation of post-translational protein modification regulation of protein modification process regulation of protein ubiquitination regulation of primary metabolic process protein ubiquitination negative regulation of protein modification process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of protein localization to plasma membrane regulation of localization cellular localization regulation of protein localization localization intracellular protein localization regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of protein localization to plasma membrane response to ischemia catabolic process autophagy process utilizing autophagic mechanism regulation of protein complex stability regulation of biological quality macroautophagy aggrephagy apoptotic process cell death programmed cell death protein catabolic process macromolecule catabolic process cellular response to stress response to mitochondrial depolarisation establishment of protein localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle protein import into nucleus intracellular protein transport fat cell proliferation cell population proliferation brown fat cell proliferation RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process vesicle organization cellular component organization organelle organization endosome organization cellular component organization or biogenesis endomembrane system organization developmental process cellular developmental process cell differentiation positive regulation of cell communication modulation of chemical synaptic transmission long-term synaptic potentiation synaptic signaling positive regulation of long-term synaptic potentiation regulation of synaptic plasticity trans-synaptic signaling cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation positive regulation of signaling multicellular organismal process multicellular organismal-level homeostasis homeostatic process energy homeostasis protein targeting to vacuole involved in autophagy protein targeting establishment of protein localization to vacuole protein targeting to vacuole protein localization to vacuole vacuolar transport autophagy of peroxisome pexophagy negative regulation of ferroptosis negative regulation of programmed cell death regulation of programmed cell death regulation of ferroptosis ferroptosis temperature homeostasis mitophagy autophagy of mitochondrion cellular component biogenesis cellular component assembly organelle assembly membraneless organelle assembly intracellular signal transduction canonical NF-kappaB signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of canonical NF-kappaB signal transduction protein localization to perinuclear region of cytoplasm	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle cell projection sperm midpiece organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection synapse cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle cell projection sperm midpiece organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection synapse cell junction glutamatergic synapse intracellular organelle vacuole autophagosome intracellular membrane-bounded organelle intracellular membraneless organelle sarcomere membraneless organelle contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex amphisome autolysosome lytic vacuole secondary lysosome lysosome phagophore assembly site mitochondrion inclusion body aggresome Lewy body endosome intracellular vesicle endomembrane system cytoplasmic vesicle late endosome vesicle cytoplasmic ribonucleoprotein granule ribonucleoprotein granule P-body endoplasmic reticulum nucleus membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm organelle lumen PML body nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR043145	Zinc finger, ZZ-type superfamily	Homologous Superfamily
A, B	IPR000433	Zinc finger, ZZ-type	Domain
A, B	IPR033741	Sequestosome-1, UBA domain	Domain
A, B	IPR053793	PB1-like domain	Domain
A, B	IPR009060	UBA-like superfamily	Homologous Superfamily
A, B	IPR000270	PB1 domain	Domain
A, B	IPR052260	Autophagy Receptor and Signaling Regulator	Family
A, B	IPR015940	Ubiquitin-associated domain	Domain
A, B	IPR034866	Sequestosome-1, PB1 domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.