9H1J | pdb_00009h1j

Crystal structure of the p62 UBA domain bound to VHH 6C10

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	UBA-like	8034756	3001235	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	UBA-like	8034756	3001235	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	UBA-like	8034756	3001235	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	UBA-like	8034756	3001235	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, B, C, D	Heavy Chain	IGHV5	-	sequestosome-1	SAbDab (2026-01-23)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	Sequestosome-1	protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding binding molecular sequestering activity ubiquitin-modified protein reader activity ubiquitin-like protein reader activity protein tyrosine kinase binding protein binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding binding molecular sequestering activity ubiquitin-modified protein reader activity ubiquitin-like protein reader activity protein tyrosine kinase binding protein binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding identical protein binding molecular transducer activity signaling receptor activity signaling adaptor activity SH2 domain binding protein domain specific binding molecular condensate scaffold activity ubiquitin binding ubiquitin-like protein binding ionotropic glutamate receptor binding glutamate receptor binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding protein sequestering activity protein kinase C 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 localization macromolecule localization intracellular protein localization 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 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 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 positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process protein catabolic process macromolecule catabolic process cellular response to stress response to mitochondrial depolarisation small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction Ras protein signal transduction intracellular signal transduction regulation of intracellular signal transduction regulation of Ras protein signal transduction intracellular signaling cassette 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 proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process fat cell proliferation cell population proliferation brown fat cell proliferation vesicle-mediated transport endosomal transport regulation of cellular component organization regulation of organelle organization cellular component organization organelle organization regulation of mitochondrion organization cellular component organization or biogenesis mitochondrion organization 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 DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process vesicle organization endosome organization 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 ferroptosis ferroptosis autophagy of mitochondrion temperature homeostasis mitophagy cellular component biogenesis cellular component assembly organelle assembly membraneless organelle assembly canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction protein localization to perinuclear region of cytoplasm	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell projection extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell projection sperm midpiece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection inclusion body 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 aggresome nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen Lewy body endosome intracellular vesicle endomembrane system cytoplasmic vesicle late endosome cytoplasmic ribonucleoprotein granule ribonucleoprotein granule P-body endoplasmic reticulum nuclear body PML body
A, B, C, D	VHH 6C10	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	Pharos: Q13501	amyotrophic lateral sclerosis frontotemporal dementia and/or amyotrophic lateral sclerosis 3 neurodegeneration with ataxia, dystonia, and gaze palsy, childhood-onset bone Paget disease Paget disease of bone 3 age-related macular degeneration neurodegenerative disease behavioral variant of frontotemporal dementia NONAKA MYOPATHY Paget disease of bone 2, early-onset pancreatic intraductal papillary-mucinous carcinoma sarcoma tuberculosis GNE myopathy large cell medulloblastoma amyotrophic lateral sclerosis frontotemporal dementia and/or amyotrophic lateral sclerosis 3 neurodegeneration with ataxia, dystonia, and gaze palsy, childhood-onset bone Paget disease Paget disease of bone 3 age-related macular degeneration neurodegenerative disease behavioral variant of frontotemporal dementia NONAKA MYOPATHY Paget disease of bone 2, early-onset pancreatic intraductal papillary-mucinous carcinoma sarcoma tuberculosis GNE myopathy large cell medulloblastoma medulloblastoma osteosarcoma pituitary cancer spina bifida Alzheimer disease cancer hepatocellular carcinoma lung cancer myopathy, distal, with rimmed vacuoles non-small cell lung carcinoma ovarian cancer pancreatic ductal adenocarcinoma psoriasis subependymal giant cell astrocytoma distal myopathy frontotemporal dementia with motor neuron disease malignant mesothelioma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.