6XX0 | pdb_00006xx0

Crystal structure of NEMO in complex with Ubv-LIN

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d6xx0d_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6xx0c_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	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)
B	SCOP2B Superfamily	NEMO CC2-LZ-like	8090864	3002465	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	NEMO CC2-LZ-like	8090864	3002465	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)
D	Ribosomal_L36	e6xx0D1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Ribosomal_L36	ECOD (v294.1)
C	Ribosomal_L36	e6xx0C1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Ribosomal_L36	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Ubv-LIN	-	-	-
A, B	Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_b	protein binding binding protein domain specific binding protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity protein heterodimerization activity protein dimerization activity transferrin receptor binding signaling receptor binding ubiquitin binding ubiquitin-like protein binding linear polyubiquitin binding polyubiquitin modification-dependent protein binding protein binding binding protein domain specific binding protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity protein heterodimerization activity protein dimerization activity transferrin receptor binding signaling receptor binding ubiquitin binding ubiquitin-like protein binding linear polyubiquitin binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding identical protein binding protein homodimerization activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis positive regulation of cell communication regulation of cellular process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling immune response-regulating cell surface receptor signaling pathway 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 cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process catabolic process positive regulation of protein metabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process protein metabolic process regulation of protein metabolic process primary metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of canonical NF-kappaB signal transduction negative regulation of cell communication negative regulation of cellular process negative regulation of response to stimulus negative regulation of signal transduction apoptotic process cell death programmed cell death biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism innate immune response response to external biotic stimulus regulation of cellular response to stress regulation of response to endoplasmic reticulum stress negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway regulation of programmed cell death intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress regulation of intrinsic apoptotic signaling pathway regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway regulation of response to stress negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway response to endoplasmic reticulum stress negative regulation of response to endoplasmic reticulum stress negative regulation of programmed cell death regulation of apoptotic process apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process regulation of apoptotic signaling pathway multicellular organismal process B cell homeostasis multicellular organismal-level homeostasis leukocyte homeostasis homeostatic process homeostasis of number of cells lymphocyte homeostasis defense response to bacterium response to bacterium positive regulation of T cell receptor signaling pathway regulation of antigen receptor-mediated signaling pathway regulation of T cell receptor signaling pathway positive regulation of antigen receptor-mediated signaling pathway positive regulation of autophagy macroautophagy autophagy regulation of autophagy regulation of macroautophagy positive regulation of macroautophagy process utilizing autophagic mechanism response to virus vesicle localization establishment of organelle localization localization cellular localization organelle localization establishment of vesicle localization establishment of localization in cell establishment of localization inflammatory response anoikis positive regulation of DNA-templated transcription RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton cytoplasm cytosol mitotic spindle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton cytoplasm cytosol mitotic spindle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex catalytic complex IkappaB kinase complex transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups serine/threonine protein kinase complex ubiquitin ligase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR034735	NEMO, Zinc finger	Domain
A, B	IPR021063	NF-kappa-B essential modulator NEMO, N-terminal	Domain
A, B	IPR032419	NF-kappa-B essential modulator NEMO, CC2-LZ domain	Domain
A, B	IPR051301	Optineurin/NF-kappa-B Essential Modulator	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9Y6K9	incontinentia pigmenti immunodeficiency without anhidrotic ectodermal dysplasia osteopetrosis anhidrotic ectodermal dysplasia-immunodeficiency-osteopetrosis-lymphedema syndrome immunodeficiency 33 non-alcoholic fatty liver disease ectodermal dysplasia and immune deficiency Invasive pneumococcal disease, recurrent isolated, 2 ectodermal dysplasia and immunodeficiency 1 nevus of Ito ectodermal dysplasia syndrome intellectual disability Ito hypomelanosis lymphatic system disease hyper-IgM syndrome type 1 incontinentia pigmenti immunodeficiency without anhidrotic ectodermal dysplasia osteopetrosis anhidrotic ectodermal dysplasia-immunodeficiency-osteopetrosis-lymphedema syndrome immunodeficiency 33 non-alcoholic fatty liver disease ectodermal dysplasia and immune deficiency Invasive pneumococcal disease, recurrent isolated, 2 ectodermal dysplasia and immunodeficiency 1 nevus of Ito ectodermal dysplasia syndrome intellectual disability Ito hypomelanosis lymphatic system disease hyper-IgM syndrome type 1 lung benign neoplasm

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.