3VUX | pdb_00003vux

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

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d3vuxc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3vuxb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3vuxa_	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)
C	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
A	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)
F [auth G]	ATG7_N	e3vuxG1	A: alpha bundles	X: Coronavirus nsp1	H: Coronavirus nsp1	T: Coronavirus nsp1	F: ATG7_N	ECOD (develop294)
E [auth F]	V-set	e3vuxF1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
D [auth E]	V-set	e3vuxE1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
C	RRM_1	e3vuxC1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)
B	RRM_1	e3vuxB1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)
A	Ribosomal_S7	e3vuxA1	A: alpha bundles	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: Ribosomal_S7	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	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)
A	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
D [auth E], E [auth F], F [auth G]	PF01754	A20-like zinc finger (zf-A20)	A20-like zinc finger	-	Family
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth E], E [auth F], F [auth G]	Tumor necrosis factor alpha-induced protein 3	DNA binding 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 DNA binding 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 defense response response to other organism biological regulation response to external stimulus response to biotic stimulus regulation of defense response to virus defense response to virus regulation of response to stimulus response to stress 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 defense response response to other organism biological regulation response to external stimulus response to biotic stimulus regulation of defense response to virus defense response to virus regulation of response to stimulus 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 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 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 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 multicellular organismal process regulation of tumor necrosis factor production negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process tumor necrosis factor superfamily cytokine production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production 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 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 intracellular signal transduction cytoplasmic pattern recognition receptor signaling pathway intracellular receptor signaling pathway negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction regulation of cytoplasmic pattern recognition receptor signaling pathway endolysosomal toll-like receptor signaling pathway regulation of intracellular signal transduction 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 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 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 response to peptide 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 canonical NF-kappaB 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 protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of 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 regulation of chronic inflammatory response chronic inflammatory response negative regulation of chronic inflammatory response protein deubiquitination involved in ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species 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 positive regulation of epithelial cell proliferation hepatocyte proliferation positive regulation of hepatocyte proliferation regulation of epithelial cell proliferation epithelial cell proliferation localization establishment of protein localization establishment of protein localization to organelle establishment of protein localization to vacuole establishment of localization 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 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 endothelial cell apoptotic process regulation of endothelial cell apoptotic process	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 intracellular organelle 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 intracellular organelle lytic vacuole vacuole intracellular membrane-bounded organelle lysosome nucleus
A, B, C	Polyubiquitin-C	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding nucleic acid binding	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule 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 intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure 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 intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
D [auth E], E [auth F], F [auth G]	IPR051346	OTU Domain-Containing Deubiquitinase	Family
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	IPR050158	Ubiquitin and ubiquitin-like	Family
A, B, C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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
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

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.