3VUW

Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3vuwa_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3vuwb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3vuwc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	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)
A	ubiquitin_1	e3vuwA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	ubiquitin_1	e3vuwB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
C	ubiquitin_1	e3vuwC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D [auth E]	zf-A20	e3vuwE1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: A20-like zinc finger (From Topology)	T: A20-like zinc finger	F: zf-A20	ECOD (1.6)
E [auth F]	zf-A20	e3vuwF1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: A20-like zinc finger (From Topology)	T: A20-like zinc finger	F: zf-A20	ECOD (1.6)
F [auth G]	zf-A20	e3vuwG1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: A20-like zinc finger (From Topology)	T: A20-like zinc finger	F: zf-A20	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	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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
D [auth E], E [auth F], F [auth G]	PF01754	A20-like zinc finger (zf-A20)	A20-like zinc finger	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Polyubiquitin-C	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding RNA binding organic cyclic compound binding nucleic acid binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
D [auth E], E [auth F], F [auth G]	Tumor necrosis factor alpha-induced protein 3	DNA binding binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding enzyme binding protease binding ubiquitin binding ubiquitin-like protein binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding K63-linked deubiquitinase activity DNA binding binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding enzyme binding protease binding ubiquitin binding ubiquitin-like protein binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding K63-linked deubiquitinase activity ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity kinase binding cysteine-type peptidase activity cysteine-type deubiquitinase activity aminoacyltransferase activity ubiquitin-like protein transferase activity acyltransferase activity transferase activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of defense response regulation of response to biotic stimulus regulation of biological process biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus response to other organism defense response biological regulation defense response to symbiont response to external stimulus response to biotic stimulus regulation of defense response to virus defense response to virus regulation of response to stimulus regulation of defense response regulation of response to biotic stimulus regulation of biological process biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus response to other organism defense response biological regulation defense response to symbiont response to external stimulus response to biotic stimulus regulation of defense response to virus defense response to virus regulation of response to stimulus defense response to other organism response to stress regulation of response to stress regulation of defense response to virus by host response to external biotic stimulus response to virus cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process pattern recognition receptor signaling pathway negative regulation of biological process regulation of signal transduction 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 immune response immune response-activating cell surface receptor signaling pathway regulation of innate immune response regulation of toll-like receptor 4 signaling pathway 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 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 negative regulation of cellular process innate immune response 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 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 multicellular organismal process regulation of tumor necrosis factor production cellular biosynthetic process negative regulation of cellular metabolic process negative regulation of tumor necrosis factor production organic substance metabolic process cytokine production organic substance biosynthetic process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process negative regulation of metabolic process tumor necrosis factor superfamily cytokine production regulation of cellular metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process negative regulation of interleukin-2 production regulation of interleukin-2 production interleukin-2 production interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production 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 organonitrogen compound metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process primary metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal extrinsic apoptotic signaling pathway via death domain receptors regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of programmed cell death regulation of apoptotic process negative regulation of extrinsic apoptotic signaling pathway via death domain receptors cell death regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway via death domain receptors apoptotic process programmed cell death regulation of apoptotic signaling pathway cell migration cell motility negative regulation of toll-like receptor 2 signaling pathway regulation of toll-like receptor 2 signaling pathway toll-like receptor 2 signaling pathway cellular component organization organelle organization cellular component organization or biogenesis cytoskeleton organization negative regulation of tissue remodeling homeostatic process negative regulation of bone remodeling regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption negative regulation of bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis positive regulation of cell communication positive regulation of signal transduction positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of cellular process regulation of Wnt signaling pathway positive regulation of signaling CD40 signaling pathway negative regulation of CD40 signaling pathway regulation of CD40 signaling pathway cytoplasmic pattern recognition receptor signaling pathway intracellular receptor signaling pathway negative regulation of cytoplasmic pattern recognition receptor signaling pathway regulation of cytoplasmic pattern recognition receptor signaling pathway endolysosomal toll-like receptor signaling pathway negative regulation of toll-like receptor 3 signaling pathway regulation of toll-like receptor 3 signaling pathway toll-like receptor 3 signaling pathway protein polyubiquitination protein K48-linked ubiquitination regulation of leukocyte activation regulation of cell activation lymphocyte activation negative regulation of lymphocyte activation leukocyte activation regulation of B cell activation negative regulation of B cell activation B cell activation cell activation negative regulation of cell activation negative regulation of leukocyte activation regulation of lymphocyte activation protein deubiquitination protein modification by small protein removal regulation of lipopolysaccharide-mediated signaling pathway response to organic substance cellular response to lipopolysaccharide cellular response to biotic stimulus lipopolysaccharide-mediated signaling pathway multicellular organism development response to bacterium anatomical structure development system development developmental process tolerance induction to lipopolysaccharide cellular response to molecule of bacterial origin cellular response to oxygen-containing compound response to chemical negative regulation of response to external stimulus cellular response to lipid response to molecule of bacterial origin tolerance induction immune system development negative regulation of lipopolysaccharide-mediated signaling pathway response to lipid negative regulation of response to biotic stimulus cellular response to organic substance response to oxygen-containing compound response to lipopolysaccharide cellular response to chemical stimulus response to cytokine cytokine-mediated signaling pathway cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway regulation of response to cytokine stimulus response to tumor necrosis factor regulation of developmental process angiogenesis regulation of vasculature development regulation of response to wounding tube morphogenesis vascular wound healing response to wounding regulation of anatomical structure morphogenesis blood vessel development wound healing regulation of multicellular organismal development blood vessel morphogenesis tube development angiogenesis involved in wound healing vasculature development circulatory system development anatomical structure morphogenesis regulation of angiogenesis regulation of wound healing anatomical structure formation involved in morphogenesis regulation of vascular wound healing negative regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway nucleotide-binding oligomerization domain containing 2 signaling pathway regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction negative regulation of immune response negative regulation of defense response negative regulation of innate immune response negative regulation of inflammatory response regulation of inflammatory response inflammatory response interleukin-1 production regulation of interleukin-1 beta production negative regulation of interleukin-1 beta production negative regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production negative regulation of cell population proliferation cell population proliferation regulation of smooth muscle cell proliferation smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation catabolic process positive regulation of protein metabolic process macromolecule catabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process organonitrogen compound catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process organic substance catabolic process regulation of protein catabolic process protein K63-linked deubiquitination adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of germinal center formation regulation of adaptive immune response adaptive immune response regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains germinal center formation negative regulation of DNA-binding transcription factor activity RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process negative regulation of NF-kappaB transcription factor activity nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of molecular function nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of molecular function organic cyclic compound metabolic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process regulation of DNA-templated transcription chronic inflammatory response regulation of chronic inflammatory response negative regulation of chronic inflammatory response cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to inorganic substance response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to stress negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway nucleotide-binding oligomerization domain containing 1 signaling pathway regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway regulation of hepatocyte proliferation positive regulation of cell population proliferation gland development liver development gland morphogenesis animal organ morphogenesis epithelial cell proliferation liver morphogenesis positive regulation of epithelial cell proliferation animal organ development epithelial cell proliferation involved in liver morphogenesis hepatocyte proliferation hepaticobiliary system development positive regulation of hepatocyte proliferation regulation of epithelial cell proliferation protein localization establishment of protein localization cellular localization establishment of protein localization to vacuole protein localization to vacuole establishment of localization localization establishment of protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to organelle protein K11-linked deubiquitination protein K48-linked deubiquitination toll-like receptor 5 signaling pathway negative regulation of toll-like receptor 5 signaling pathway regulation of toll-like receptor 5 signaling pathway response to organonitrogen compound response to muramyl dipeptide response to nitrogen compound B cell homeostasis leukocyte homeostasis B-1 B cell homeostasis homeostasis of number of cells lymphocyte homeostasis regulation of leukocyte proliferation negative regulation of osteoclast proliferation osteoclast proliferation regulation of osteoclast proliferation leukocyte proliferation negative regulation of leukocyte proliferation negative regulation of endothelial cell apoptotic process regulation of epithelial cell apoptotic process epithelial cell apoptotic process negative regulation of epithelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process proteolysis	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle lytic vacuole vacuole intracellular membrane-bounded organelle lysosome nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR019954	Ubiquitin conserved site	Conserved Site
A, B, C	IPR000626	Ubiquitin-like domain	Domain
A, B, C	IPR019956	Ubiquitin domain	Domain
A, B, C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
D [auth E], E [auth F], F [auth G]	IPR003323	OTU domain	Domain
D [auth E], E [auth F], F [auth G]	IPR002653	Zinc finger, A20-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer
D [auth E], E [auth F], F [auth G]	Pharos: P21580	rheumatoid arthritis psoriasis systemic lupus erythematosus autoimmune disease follicular lymphoma hereditary pediatric Behçet-like disease Inflammation multiple sclerosis Sjogren syndrome primary cutaneous T-cell non-Hodgkin lymphoma juvenile idiopathic arthritis primitive neuroectodermal tumor pustulosis palmaris et plantaris sinusitis lung carcinoma rheumatoid arthritis psoriasis systemic lupus erythematosus autoimmune disease follicular lymphoma hereditary pediatric Behçet-like disease Inflammation multiple sclerosis Sjogren syndrome primary cutaneous T-cell non-Hodgkin lymphoma juvenile idiopathic arthritis primitive neuroectodermal tumor pustulosis palmaris et plantaris sinusitis lung carcinoma skin disease lymphoma acute myeloid leukemia ulcerative colitis malignant glioma diabetes mellitus pancreatic ductal adenocarcinoma granulomatous slack skin disease pituitary cancer hereditary periodic fever syndrome interstitial cystitis lung adenocarcinoma lupus erythematosus spina bifida systemic sclerosis allergic rhinitis malignant mesothelioma cutaneous lupus erythematosus esophageal adenocarcinoma non-small cell lung carcinoma gastric carcinoma periodic fever syndrome lung cancer subependymal giant cell astrocytoma tuberculosis atypical teratoid rhabdoid tumor bipolar disorder malignant ependymoma medulloblastoma cystic fibrosis myositis ovarian cancer glioblastoma pilocytic astrocytoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.