7OWD

Structure of CYLD CAP-Gly3 (467-552) bound to Ub; tetragonal space group

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Cap-Gly domain	8042547	3000882	SCOP2B (2022-06-29)
B [auth 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)
A [auth B]	CAP_GLY	e7owdB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CAP_GLY	ECOD (1.6)
B [auth A]	ubiquitin_1	e7owdA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF16607	Phosphorylation region of CYLD, unstructured (CYLD_phos_site)	Phosphorylation region of CYLD, unstructured	-	Disordered
A [auth B]	PF01302	CAP-Gly domain (CAP_GLY)	CAP-Gly domain	Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP ...	Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein Swiss:Q20728 CAP-Gly domain was recently solved [2]. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove [2].	Domain
B [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Ubiquitin carboxyl-terminal hydrolase CYLD	protein binding binding proline-rich region binding ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity K48-linked deubiquitinase activity catalytic activity deubiquitinase activity cysteine-type peptidase activity cysteine-type deubiquitinase activity Met1-linked polyubiquitin deubiquitinase activity K63-linked deubiquitinase activity protein binding binding proline-rich region binding ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity K48-linked deubiquitinase activity catalytic activity deubiquitinase activity cysteine-type peptidase activity cysteine-type deubiquitinase activity Met1-linked polyubiquitin deubiquitinase activity K63-linked deubiquitinase activity kinase binding enzyme binding protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	multicellular organismal process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of type I interferon production organic substance metabolic process cytokine production organic substance biosynthetic process negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process multicellular organismal process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of type I interferon production organic substance metabolic process cytokine production organic substance biosynthetic process negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process type I interferon production cellular metabolic process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production CD4-positive or CD8-positive, alpha-beta T cell lineage commitment developmental process cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation T cell lineage commitment lymphocyte activation lymphocyte differentiation leukocyte activation T cell activation immune system process cell differentiation positive T cell selection anatomical structure development T cell differentiation T cell selection cell fate commitment leukocyte differentiation cellular response to stimulus response to stimulus signaling regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication regulation of intracellular signal transduction signal transduction intrinsic apoptotic signaling pathway regulation of signaling regulation of apoptotic process cell death apoptotic signaling pathway regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway protein-containing complex organization necroptotic process ripoptosome assembly involved in necroptotic process programmed necrotic cell death ripoptosome assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly cellular component organization or biogenesis negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of cell communication negative regulation of Wnt signaling pathway Wnt signaling pathway cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus response to organic substance response to interleukin-18 response to cytokine cytokine-mediated signaling pathway negative regulation of interleukin-18-mediated signaling pathway cellular response to cytokine stimulus cellular response to organic substance cellular response to interleukin-18 regulation of cytokine-mediated signaling pathway interleukin-18-mediated signaling pathway regulation of response to cytokine stimulus cellular response to chemical stimulus negative regulation of response to cytokine stimulus negative regulation of cytokine-mediated signaling pathway response to chemical regulation of interleukin-18-mediated signaling pathway positive regulation of cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of signal transduction positive regulation of T cell receptor signaling pathway positive regulation of biological process regulation of antigen receptor-mediated signaling pathway positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process positive regulation of cellular process immune response-activating cell surface receptor signaling pathway regulation of T cell receptor signaling pathway T cell receptor signaling pathway regulation of immune response antigen receptor-mediated signaling pathway activation of immune response positive regulation of antigen receptor-mediated signaling pathway positive regulation of signaling regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cilium assembly cilium organization organelle assembly plasma membrane bounded cell projection organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of organelle organization regulation of plasma membrane bounded cell projection assembly regulation of cilium assembly organelle organization regulation of organelle assembly cell projection assembly regulation of plasma membrane bounded cell projection organization regulation of necroptotic process regulation of programmed necrotic cell death protein deubiquitination organonitrogen compound metabolic process primary metabolic process protein modification by small protein removal macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway regulation of tumor necrosis factor-mediated signaling pathway response to tumor necrosis factor regulation of mitotic cell cycle cell cycle regulation of cell cycle mitotic cell cycle multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells negative regulation of intracellular signal transduction negative regulation of p38MAPK cascade p38MAPK cascade intracellular signaling cassette regulation of MAPK cascade regulation of p38MAPK cascade MAPK cascade negative regulation of MAPK cascade regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response regulation of inflammatory response negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of programmed cell death positive regulation of extrinsic apoptotic signaling pathway positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway regulation of leukocyte differentiation regulation of developmental process regulation of leukocyte activation regulation of cell activation regulation of cell differentiation regulation of cell development regulation of B cell differentiation multicellular organism development B cell differentiation regulation of B cell activation regulation of lymphocyte differentiation regulation of multicellular organismal development B cell activation regulation of hemopoiesis regulation of lymphocyte activation negative regulation of JNK cascade JNK cascade regulation of JNK cascade negative regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary 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 regulation of cytoskeleton organization microtubule cytoskeleton organization regulation of microtubule-based process microtubule-based process regulation of microtubule cytoskeleton organization cytoskeleton organization protein linear deubiquitination protein localization regulation of localization cellular localization regulation of protein localization localization regulation of cellular localization cellular macromolecule localization macromolecule localization positive regulation of protein localization regulation of non-canonical NF-kappaB signal transduction negative regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction proteolysis positive regulation of T cell differentiation positive regulation of developmental process positive regulation of cell activation positive regulation of leukocyte activation positive regulation of T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of hemopoiesis positive regulation of cell differentiation regulation of cell-cell adhesion positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle cell projection organelle ciliary tip cilium plasma membrane bounded cell projection perinuclear region of cytoplasm intracellular organelle cytoskeleton spindle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle cell projection organelle ciliary tip cilium plasma membrane bounded cell projection perinuclear region of cytoplasm intracellular organelle cytoskeleton spindle intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle ciliary basal body microtubule organizing center polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex centrosome cell periphery plasma membrane membrane
B [auth A]	Ubiquitin	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A [auth B]	IPR036859	CAP Gly-rich domain superfamily	Homologous Superfamily
A [auth B]	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A [auth B]	IPR028889	Ubiquitin specific protease domain	Domain
A [auth B]	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A [auth B]	IPR000938	CAP Gly-rich domain	Domain
B [auth A]	IPR019954	Ubiquitin conserved site	Conserved Site
B [auth A]	IPR000626	Ubiquitin-like domain	Domain
B [auth A]	IPR019956	Ubiquitin domain	Domain
B [auth A]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	Pharos: Q9NQC7	Brooke-Spiegler syndrome thymoma listeriosis non-small cell lung carcinoma familial cylindromatosis amyotrophic lateral sclerosis trichoepithelioma, multiple familial, 1 thymic carcinoma hepatocellular carcinoma large cell medulloblastoma Liver carcinoma malignant glioma myopathy oligodendroglioma Pick disease Brooke-Spiegler syndrome thymoma listeriosis non-small cell lung carcinoma familial cylindromatosis amyotrophic lateral sclerosis trichoepithelioma, multiple familial, 1 thymic carcinoma hepatocellular carcinoma large cell medulloblastoma Liver carcinoma malignant glioma myopathy oligodendroglioma Pick disease breast cancer rheumatoid arthritis cervical cancer dermatomyositis ulcerative colitis familial multiple trichoepithelioma head and neck carcinoma inflammatory bowel disease leprosy lung cancer malignant mesothelioma neurodegenerative disease osteosarcoma primitive neuroectodermal tumor Sjogren syndrome Crohn disease glioblastoma head and neck neoplasm juvenile dermatomyositis malignant ependymoma medulloblastoma ovarian cancer atypical teratoid rhabdoid tumor psoriasis cancer cutaneous lupus erythematosus tuberculosis head and neck cancer
B [auth A]	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 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.