2KNB | pdb_00002knb

Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
A	d2knba_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d2knbb_	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ubiquitin-related	8066172	4000962	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ubiquitin-like	8066173	3000157	SCOP2 (2022-06-29)
B	SCOP2 Family	SH3-domain	8065216	4000369	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	SH3-domain	8065217	3000153	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ubiquitin_2	e2knbA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_2	ECOD (1.6)
B	SH3_1	e2knbB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
B	PF00018	SH3 domain (SH3_1)	SH3 domain	SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	E3 ubiquitin-protein ligase parkin	histone deacetylase binding protein binding binding enzyme binding heat shock protein binding protein-folding chaperone binding protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding cullin family protein binding PDZ domain binding protein domain specific binding ubiquitin binding ubiquitin-like protein binding histone deacetylase binding protein binding binding enzyme binding heat shock protein binding protein-folding chaperone binding protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding cullin family protein binding PDZ domain binding protein domain specific binding ubiquitin binding ubiquitin-like protein binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity ubiquitin-like protein conjugating enzyme binding ubiquitin conjugating enzyme binding kinase binding protein kinase binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity beta-catenin binding signaling receptor binding G protein-coupled receptor binding F-box domain binding ubiquitin-like protein ligase activity ubiquitin protein ligase activity ubiquitin-specific protease binding protease binding identical protein binding phospholipase binding cytoskeletal protein binding tubulin binding Hsp70 protein binding actin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	response to stimulus response to activity response to muscle activity response to chemical response to xenobiotic stimulus cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus response to stimulus response to activity response to muscle activity response to chemical response to xenobiotic stimulus cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of tumor necrosis factor-mediated signaling pathway positive regulation of response to stimulus cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway biological regulation response to peptide regulation of response to cytokine stimulus regulation of response to stimulus regulation of cell communication cellular process response to tumor necrosis factor positive regulation of cytokine-mediated signaling pathway positive regulation of signaling regulation of protein stability regulation of biological quality protein stabilization import into cell regulation of localization positive regulation of neurotransmitter transport transport regulation of transport regulation of neurotransmitter transport neurotransmitter transport establishment of localization localization positive regulation of transport positive regulation of neurotransmitter uptake neurotransmitter uptake regulation of neurotransmitter uptake regulation of amine metabolic process dopamine metabolic process primary metabolic process catechol-containing compound metabolic process regulation of primary metabolic process amine metabolic process catecholamine metabolic process phenol-containing compound metabolic process metabolic process regulation of catecholamine metabolic process regulation of metabolic process biogenic amine metabolic process regulation of dopamine metabolic process response to topologically incorrect protein response to stress response to unfolded protein negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway regulation of signal transduction by p53 class mediator negative regulation of cellular process intrinsic apoptotic signaling pathway negative regulation of signal transduction by p53 class mediator negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process signal transduction by p53 class mediator cell death negative regulation of signal transduction apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator intrinsic apoptotic signaling pathway by p53 class mediator apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death regulation of apoptotic signaling pathway regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process negative regulation of phosphorylation protein autoubiquitination protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process protein catabolic process macromolecule catabolic process cellular localization regulation of cellular component organization synaptic vesicle cycle regulation of synaptic vesicle recycling vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse cellular component organization synaptic vesicle recycling regulation of synaptic vesicle endocytosis establishment of localization in cell cellular component organization or biogenesis regulation of endocytosis synaptic vesicle endocytosis regulation of vesicle-mediated transport endocytosis response to oxidative stress cellular response to chemical stimulus cellular response to stress cellular response to oxidative stress cellular response to chemical stress response to ketone response to lipid response to endogenous stimulus response to alcohol response to glucocorticoid response to oxygen-containing compound response to corticosterone response to mineralocorticoid response to corticosteroid response to hormone response to steroid hormone protein K6-linked ubiquitination protein polyubiquitination proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process positive regulation of organelle organization positive regulation of cellular component organization regulation of developmental process positive regulation of developmental process anatomical structure development regulation of mitochondrial fusion mitochondrial fusion regulation of anatomical structure morphogenesis positive regulation of mitochondrial fusion mitochondrion organization developmental process regulation of organelle organization organelle fusion anatomical structure morphogenesis organelle organization regulation of mitochondrion organization startle response multicellular organismal process system process nervous system process neuromuscular process response to external stimulus cellular response to acid chemical cellular response to nitrogen compound cellular response to amino acid stimulus cellular response to L-glutamine response to L-glutamine response to nitrogen compound response to amino acid cellular response to oxygen-containing compound response to acid chemical reactive oxygen species metabolic process negative regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process protein K48-linked ubiquitination cellular response to toxic substance response to toxic substance modulation of chemical synaptic transmission synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic negative regulation of synaptic transmission synaptic signaling trans-synaptic signaling cell-cell signaling chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling negative regulation of synaptic transmission, glutamatergic cellular component biogenesis cellular component assembly aggresome assembly inclusion body assembly 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 cellular homeostasis neuron cellular homeostasis homeostatic process response to endoplasmic reticulum stress regulation of growth developmental growth cell projection organization neuron projection development regulation of cell morphogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of developmental growth system development nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of dendrite extension cellular developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis neurogenesis dendrite extension neuron projection extension regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth regulation of dendrite extension positive regulation of cell growth regulation of cell growth positive regulation of growth neuron development regulation protein catabolic process at synapse regulation of catabolic process regulation protein catabolic process at presynapse positive regulation of canonical NF-kappaB signal transduction intracellular signaling cassette positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction negative regulation by host of viral genome replication modulation by host of viral process biological process involved in interspecies interaction between organisms viral genome replication viral process viral life cycle negative regulation by host of viral process modulation of process of another organism host-mediated perturbation of symbiont process modulation by host of viral genome replication regulation of mitochondrial membrane potential regulation of membrane potential regulation of cellular response to stress regulation of cellular response to oxidative stress regulation of response to stress regulation of response to oxidative stress regulation of response to endoplasmic reticulum stress negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway negative regulation of response to endoplasmic reticulum stress exosomal secretion establishment of organelle localization negative regulation of transport secretion by cell regulation of secretion by cell negative regulation of secretion negative regulation of exocytosis negative regulation of exosomal secretion organelle localization negative regulation of secretion by cell vesicle localization secretion regulation of exosomal secretion establishment of vesicle localization export from cell extracellular exosome biogenesis regulation of secretion exocytosis extracellular vesicle biogenesis regulation of exocytosis positive regulation of mitochondrial membrane potential positive regulation of membrane potential proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process cellular response to metal ion response to metal ion cellular response to manganese ion response to manganese ion protein localization negative regulation of protein transport establishment of protein localization nitrogen compound transport cellular macromolecule localization negative regulation of hormone secretion regulation of peptide hormone secretion negative regulation of peptide hormone secretion regulation of hormone levels establishment of protein localization to extracellular region negative regulation of establishment of protein localization protein secretion regulation of protein secretion negative regulation of protein secretion regulation of hormone secretion regulation of protein localization regulation of peptide secretion hormone secretion protein localization to extracellular region negative regulation of peptide secretion peptide secretion amide transport signal release negative regulation of protein localization regulation of peptide transport regulation of establishment of protein localization regulation of protein transport peptide transport negative regulation of insulin secretion protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion mitochondrial fragmentation involved in apoptotic process apoptotic mitochondrial changes vesicle budding from membrane vesicle organization regulation of endosome organization endosome organization endomembrane system organization membrane organization negative regulation of cellular component organization negative regulation of intralumenal vesicle formation intralumenal vesicle formation negative regulation of organelle organization negative regulation of endosome organization regulation of intralumenal vesicle formation mitophagy macroautophagy type 2 mitophagy autophagy autophagy of mitochondrion process utilizing autophagic mechanism protein K63-linked ubiquitination mitochondrion localization norepinephrine metabolic process organelle fission mitochondrial fission regulation of mitochondrial fission positive regulation of mitochondrial fission protein K11-linked ubiquitination protein localization to organelle protein localization to mitochondrion regulation of post-translational protein modification regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal positive regulation of protein metabolic process positive regulation of protein linear polyubiquitination positive regulation of post-translational protein modification positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process positive regulation of protein modification by small protein conjugation or removal regulation of protein linear polyubiquitination positive regulation of protein ubiquitination regulation of protein polyubiquitination positive regulation of protein polyubiquitination protein linear polyubiquitination negative regulation of gene expression regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding positive regulation of binding positive regulation of DNA binding cellular response to hydrogen sulfide response to hydrogen sulfide negative regulation of developmental process negative regulation of mitochondrial fission behavior learning learning or memory cognition regulation of postsynaptic membrane neurotransmitter receptor levels positive regulation of proteasomal protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process regulation of protein catabolic process protein destabilization regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly actin filament bundle organization actin filament-based process negative regulation of supramolecular fiber organization regulation of actin filament organization actin cytoskeleton organization negative regulation of cytoskeleton organization actin filament organization negative regulation of actin filament bundle assembly regulation of cellular component biogenesis regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization negative regulation of mitochondrial fusion intracellular transport mitochondrion to lysosome vesicle-mediated transport lysosomal transport mitochondrion-derived vesicle mediated transport vacuolar transport mitochondrial transport positive regulation of macromolecule biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process response to curcumin response to ether regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of Wnt signaling pathway Wnt signaling pathway regulation of Wnt signaling pathway negative regulation of canonical Wnt signaling pathway positive regulation of programmed cell death positive regulation of apoptotic process regulation of type 2 mitophagy positive regulation of type 2 mitophagy regulation of autophagy positive regulation of autophagy of mitochondrion regulation of autophagy of mitochondrion positive regulation of macroautophagy positive regulation of autophagy positive regulation of mitophagy regulation of mitophagy regulation of macroautophagy protein polymerization protein-containing complex organization free ubiquitin chain polymerization protein-containing complex assembly ubiquitin recycling negative regulation of neurotransmitter transport regulation of spontaneous neurotransmitter secretion negative regulation of spontaneous neurotransmitter secretion spontaneous synaptic transmission regulation of spontaneous synaptic transmission negative regulation of neurotransmitter secretion neurotransmitter secretion spontaneous neurotransmitter secretion signal release from synapse regulation of neurotransmitter secretion positive regulation of protein localization to membrane localization within membrane protein localization to membrane positive regulation of protein localization regulation of protein localization to membrane cellular response to L-glutamate response to L-glutamate regulation of release of cytochrome c from mitochondria negative regulation of release of cytochrome c from mitochondria release of cytochrome c from mitochondria synaptic transmission, dopaminergic intrinsic apoptotic signaling pathway in response to oxidative stress neuron apoptotic process regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of neuron apoptotic process regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway neuron intrinsic apoptotic signaling pathway in response to oxidative stress negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway regulation of neuron apoptotic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process positive regulation of phosphate metabolic process purine ribonucleoside triphosphate biosynthetic process positive regulation of nucleotide biosynthetic process regulation of nucleotide biosynthetic process regulation of ATP metabolic process ribonucleotide biosynthetic process purine nucleoside triphosphate biosynthetic process regulation of small molecule metabolic process positive regulation of purine nucleotide biosynthetic process regulation of nucleotide metabolic process small molecule metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of phosphorus metabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process ribonucleoside triphosphate biosynthetic process positive regulation of ATP metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process positive regulation of nucleotide metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process purine-containing compound biosynthetic process ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process carbohydrate derivative biosynthetic process regulation of purine nucleotide biosynthetic process nucleoside triphosphate biosynthetic process purine-containing compound metabolic process positive regulation of purine nucleotide metabolic process positive regulation of ATP biosynthetic process regulation of ATP biosynthetic process organophosphate metabolic process positive regulation of small molecule metabolic process protein monoubiquitination positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process locomotory behavior adult locomotory behavior adult behavior reactive oxygen species biosynthetic process regulation of reactive oxygen species biosynthetic process negative regulation of reactive oxygen species biosynthetic process neuron intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway negative regulation of JNK cascade JNK cascade regulation of JNK cascade regulation of MAPK cascade MAPK cascade negative regulation of MAPK cascade positive regulation of establishment of protein localization carbohydrate homeostasis positive regulation of insulin secretion involved in cellular response to glucose stimulus positive regulation of insulin secretion positive regulation of peptide hormone secretion intracellular glucose homeostasis cellular response to carbohydrate stimulus chemical homeostasis response to glucose glucose homeostasis insulin secretion involved in cellular response to glucose stimulus positive regulation of secretion by cell positive regulation of protein transport positive regulation of hormone secretion response to monosaccharide response to carbohydrate positive regulation of secretion cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus positive regulation of peptide secretion cellular response to glucose stimulus positive regulation of protein secretion response to hexose regulation of insulin secretion involved in cellular response to glucose stimulus regulation of postsynaptic membrane potential regulation of system process chemical synaptic transmission, postsynaptic modulation of excitatory postsynaptic potential regulation of multicellular organismal process regulation of nervous system process negative regulation of excitatory postsynaptic potential excitatory postsynaptic potential monoamine transport organic hydroxy compound transport dopamine transport catecholamine uptake dopamine uptake involved in synaptic transmission catecholamine transport neurotransmitter reuptake catecholamine uptake involved in synaptic transmission dopamine uptake regulation of catalytic activity negative regulation of glucokinase activity negative regulation of catalytic activity regulation of transferase activity negative regulation of hexokinase activity negative regulation of kinase activity negative regulation of transferase activity regulation of carbohydrate metabolic process negative regulation of carbohydrate metabolic process carbohydrate metabolic process negative regulation of molecular function regulation of kinase activity	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle mitochondrion-derived vesicle intracellular organelle cytoplasmic vesicle organelle vesicle Golgi membrane Golgi apparatus cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle mitochondrion-derived vesicle intracellular organelle cytoplasmic vesicle organelle vesicle Golgi membrane Golgi apparatus membrane endomembrane system bounding membrane of organelle organelle membrane transport vesicle synapse presynapse synaptic vesicle cell junction secretory vesicle exocytic vesicle protein-containing complex ubiquitin ligase complex catalytic complex Parkin-FBXW7-Cul1 ubiquitin ligase complex transferase complex intracellular protein-containing complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane dopaminergic synapse glutamatergic synapse cell projection neuron projection plasma membrane bounded cell projection perinuclear region of cytoplasm mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane somatodendritic compartment cell body neuronal cell body transport vesicle membrane vesicle membrane synaptic vesicle membrane exocytic vesicle membrane cytoplasmic vesicle membrane axon postsynapse axon terminus distal axon terminal bouton neuron projection terminus inclusion body aggresome postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse nucleus
B	Endophilin-A1	protein binding binding transmembrane transporter binding kinase binding enzyme binding protein kinase binding lipid binding identical protein binding	synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell cellular process endocytosis synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell cellular process endocytosis multicellular organismal process cellular developmental process developmental growth cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell growth cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis dendrite extension system development developmental process neuron projection extension plasma membrane bounded cell projection organization developmental cell growth growth nervous system development developmental growth involved in morphogenesis generation of neurons anatomical structure morphogenesis neuron development actin cytoskeleton organization postsynapse organization postsynaptic cytoskeleton organization organelle organization cell junction organization postsynaptic actin cytoskeleton organization actin filament-based process synapse organization cytoskeleton organization cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus cellular response to brain-derived neurotrophic factor stimulus response to nerve growth factor response to growth factor membrane organization membrane fission vesicle scission membrane bending plasma membrane tubulation regulation of biological process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization biological regulation positive regulation of biological process positive regulation of membrane tubulation regulation of plasma membrane organization plasma membrane organization endomembrane system organization positive regulation of cellular process regulation of membrane tubulation regulation of localization receptor internalization regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport regulation of receptor internalization receptor-mediated endocytosis regulation of endocytosis clathrin-dependent endocytosis regulation of clathrin-dependent endocytosis cellular component biogenesis cellular component assembly lipid tube assembly protein-containing complex organization protein-lipid complex organization protein-containing complex assembly protein-lipid complex assembly regulation of blood-brain barrier permeability system process maintenance of blood-brain barrier homeostatic process tissue homeostasis regulation of vascular permeability negative regulation of vascular permeability circulatory system process multicellular organismal-level homeostasis vascular process in circulatory system anatomical structure homeostasis regulation of biological quality blood circulation negative regulation of blood-brain barrier permeability membrane tubulation synaptic vesicle uncoating protein-containing complex disassembly vesicle uncoating cellular component disassembly clathrin coat disassembly protein depolymerization regulation of biosynthetic process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process	cytosolic region presynapse presynaptic cytosol cellular anatomical structure intracellular anatomical structure synapse cell junction cytoplasm cytosol cell periphery plasma membrane membrane glutamatergic synapse membrane-bounded organelle cytosolic region presynapse presynaptic cytosol cellular anatomical structure intracellular anatomical structure synapse cell junction cytoplasm cytosol cell periphery plasma membrane membrane glutamatergic synapse membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle neuron to neuron synapse hippocampal mossy fiber to CA3 synapse photoreceptor ribbon synapse ribbon synapse basal dendrite somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection Schaffer collateral - CA1 synapse perinuclear region of cytoplasm cell body neuronal cell body transport vesicle membrane bounding membrane of organelle vesicle membrane synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle organelle membrane exocytic vesicle postsynapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002867	IBR domain	Domain
A	IPR044066	TRIAD supradomain	Domain
A	IPR047535	E3 ubiquitin-protein ligase parkin, RING finger, HC subclass	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A	IPR041170	RING/Ubox-like zinc-binding domain	Domain
A	IPR003977	E3 ubiquitin-protein ligase parkin	Family
A	IPR047534	E3 ubiquitin-protein ligase parkin, BRcat domain	Domain
A	IPR015496	Ubiquilin	Family
A	IPR047536	E3 ubiquitin-protein ligase parkin, Rcat domain	Domain
A	IPR041565	Parkin, RING/Ubox like zinc-binding domain	Domain
A	IPR000626	Ubiquitin-like domain	Domain
A	IPR054694	E3 ubiquitin-protein ligase parkin-like, IBR domain	Domain
B	IPR004148	BAR domain	Domain
B	IPR050384	Endophilin/SH3RF	Family
B	IPR036028	SH3-like domain superfamily	Homologous Superfamily
B	IPR027267	AH/BAR domain superfamily	Homologous Superfamily
B	IPR001452	SH3 domain	Domain
B	IPR035824	Endophilin-A, SH3 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.