3BRV

NEMO/IKKb association domain structure

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: CATH
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	SCOP2B Superfamily	IKKbeta NEMO binding domain-like	8102935	3002762	SCOP2B (2022-06-29)
C	SCOP2 Family	IKKbeta NEMO binding domain-like	8047312	4005568	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	IKKbeta NEMO binding domain-like	8102935	3002762	SCOP2 (2022-06-29)
B	SCOP2 Family	NEMO IKK-binding domain-like	8046679	4005236	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	NEMO IKK-binding domain-like	8102933	3002761	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	NEMO IKK-binding domain-like	8102933	3002761	SCOP2B (2022-06-29)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	6.10.250.2110	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.20.5.390	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	L1 transposable element, trimerization domain	CATH (4.3.0)
D	1.20.5.390	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	L1 transposable element, trimerization domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF12179	I-kappa-kinase-beta NEMO binding domain (IKKbetaNEMObind)	I-kappa-kinase-beta NEMO binding domain	This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00069. These proteins are involved in inflammatory reactions. They cause release of NF-kappa-B into the nucleus o ...	This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00069. These proteins are involved in inflammatory reactions. They cause release of NF-kappa-B into the nucleus of inflammatory cells and upregulation of transcription of proinflammatory cytokines. They perform this function by phosphorylating I-kappa-B proteins which are targeted for degradation to release NF-kappa-B. This kinase (I-kappa-kinase-beta) is found in association with IKK-alpha and NEMO (NF-kappa-B essential modulator). This domain is the binding site of IKK-beta for NEMO.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Inhibitor of nuclear factor kappa-B kinase subunit beta	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity IkappaB kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups identical protein binding protein binding protein heterodimerization activity protein dimerization activity transferrin receptor binding signaling receptor binding scaffold protein binding protein serine kinase activity protein homodimerization activity kinase binding enzyme binding protein kinase binding histone H2AS1 kinase activity histone modifying activity histone H2A kinase activity histone kinase activity	regulation of biological process regulation of cellular process phosphorylation biological regulation regulation of phosphate metabolic process phosphate-containing compound metabolic process regulation of phosphorylation regulation of phosphorus metabolic process cellular process metabolic process phosphorus metabolic process regulation of metabolic process cellular response to stimulus regulation of defense response regulation of biological process regulation of cellular process phosphorylation biological regulation regulation of phosphate metabolic process phosphate-containing compound metabolic process regulation of phosphorylation regulation of phosphorus metabolic process cellular process metabolic process phosphorus metabolic process regulation of metabolic process cellular response to stimulus regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus toll-like receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus signal transduction positive regulation of immune system process innate immune response-activating signaling pathway MyD88-dependent toll-like receptor signaling pathway positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane regulation of signal transduction regulation of pattern recognition receptor signaling pathway regulation of toll-like receptor signaling pathway regulation of signaling regulation of cell communication positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process cellular component organization organelle organization actin cytoskeleton organization cortical actin cytoskeleton organization cortical cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization protein phosphorylation macromolecule modification protein metabolic process protein modification process immune response-regulating cell surface receptor signaling pathway cell surface receptor signaling pathway Fc receptor signaling pathway Fc-epsilon receptor signaling pathway peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus response to tumor necrosis factor regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway regulation of response to cytokine stimulus intracellular signal transduction cytoplasmic pattern recognition receptor signaling pathway intracellular receptor signaling pathway endolysosomal toll-like receptor signaling pathway toll-like receptor 3 signaling pathway positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction regulation of intracellular signal transduction intracellular signaling cassette positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction positive regulation of signaling immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway antigen receptor-mediated signaling pathway stress-activated MAPK cascade stress-activated protein kinase signaling cascade cellular response to stress MAPK cascade antigen processing and presentation antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of exogenous peptide antigen via MHC class I antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen bicellular tight junction assembly regulation of cellular component organization negative regulation of biological process tight junction organization cellular component biogenesis cellular component assembly negative regulation of cell junction assembly cell junction assembly negative regulation of cellular process cell-cell junction assembly cell-cell junction organization regulation of bicellular tight junction assembly negative regulation of cellular component organization apical junction assembly regulation of cellular component biogenesis regulation of cell junction assembly cell junction organization tight junction assembly negative regulation of bicellular tight junction assembly response to lectin cellular response to lectin innate immune response activating cell surface receptor signaling pathway stimulatory C-type lectin receptor signaling pathway TRIF-dependent toll-like receptor signaling pathway MyD88-independent toll-like receptor signaling pathway multicellular organismal process regulation of establishment of endothelial barrier cellular developmental process regulation of developmental process endothelium development cell development regulation of cell differentiation epithelial cell differentiation regulation of cell development regulation of epithelial cell differentiation endothelial cell development multicellular organism development cell differentiation regulation of endothelial cell development anatomical structure development regulation of multicellular organismal process developmental process epithelium development regulation of multicellular organismal development endothelial cell differentiation regulation of endothelial cell differentiation tissue development epithelial cell development establishment of endothelial barrier protein maturation response to virus cellular response to interleukin-1 interleukin-1-mediated signaling pathway response to interleukin-1 inflammatory response	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex receptor complex intracellular anatomical structure cytoplasm cytosol membrane microdomain cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex receptor complex intracellular anatomical structure cytoplasm cytosol membrane microdomain membrane raft catalytic complex IkappaB kinase complex transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups serine/threonine protein kinase complex cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B, D	NF-kappa-B essential modulator	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 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 catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process modification-dependent protein catabolic process positive regulation of proteolysis metabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process 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 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 DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription 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 positive regulation of macromolecule biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	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, C	IPR051180	Inhibitor of nuclear factor kappa-B kinase	Family
A, C	IPR000719	Protein kinase domain	Domain
A, C	IPR046375	IKBKB, scaffold dimerization domain superfamily	Homologous Superfamily
A, C	IPR022007	I-kappa-kinase-beta NEMO binding domain	Domain
A, C	IPR000626	Ubiquitin-like domain	Domain
A, C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, C	IPR041185	IKBKB, scaffold dimerization domain	Domain
A, C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, C	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B, D	IPR034735	NEMO, Zinc finger	Domain
B, D	IPR021063	NF-kappa-B essential modulator NEMO, N-terminal	Domain
B, D	IPR032419	NF-kappa-B essential modulator NEMO, CC2-LZ domain	Domain
B, D	IPR051301	Optineurin/NF-kappa-B Essential Modulator	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: O14920	severe combined immunodeficiency due to IKK2 deficiency hypertensive disorder severe combined immunodeficiency Hyperbilirubinemia, Neonatal psoriasis systemic lupus erythematosus astrocytic tumor Gaucher disease malignant ependymoma oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cancer glioblastoma osteosarcoma severe combined immunodeficiency due to IKK2 deficiency hypertensive disorder severe combined immunodeficiency Hyperbilirubinemia, Neonatal psoriasis systemic lupus erythematosus astrocytic tumor Gaucher disease malignant ependymoma oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cancer glioblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma lymphoplasmacytic lymphoma non-Hodgkin lymphoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm
B, D	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.