2DBF

Solution structure of the Death domain in human Nuclear factor NF-kappa-B p105 subunit

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DEATH domain, DD	8087283	4000378	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DEATH domain	8087284	3000069	SCOP2 (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	Death	e2dbfA1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: Death	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00531	Death domain (Death)	Death domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Nuclear factor NF-kappa-B p105 subunit	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding protein binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding cytoskeletal protein binding actinin binding	cellular response to nitrogen compound cellular response to stimulus cellular response to dsRNA response to stimulus cellular response to organic cyclic compound response to dsRNA response to nitrogen compound cellular response to chemical stimulus response to chemical cellular process response to organic cyclic compound response to peptide cellular response to interleukin-17 response to interleukin-17 cellular response to nitrogen compound cellular response to stimulus cellular response to dsRNA response to stimulus cellular response to organic cyclic compound response to dsRNA response to nitrogen compound cellular response to chemical stimulus response to chemical cellular process response to organic cyclic compound response to peptide cellular response to interleukin-17 response to interleukin-17 response to cytokine cellular response to cytokine stimulus developmental process multicellular organismal process mammary gland morphogenesis mammary gland development gland development animal organ development anatomical structure morphogenesis gland morphogenesis tissue remodeling anatomical structure development mammary gland involution animal organ morphogenesis apoptotic process cell death programmed cell death 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 immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation positive regulation of biological process RNA metabolic process positive regulation of miRNA metabolic process primary metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of metabolic process regulation of RNA metabolic process regulation of miRNA metabolic process metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process macromolecule metabolic process miRNA metabolic process regulation of metabolic process regulation of cellular process signaling non-canonical NF-kappaB signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction negative regulation of small molecule metabolic process negative regulation of calcidiol 1-monooxygenase activity regulation of catalytic activity fat-soluble vitamin metabolic process regulation of hormone biosynthetic process regulation of lipid metabolic process negative regulation of biological process negative regulation of catalytic activity vitamin biosynthetic process negative regulation of lipid biosynthetic process negative regulation of cellular metabolic process vitamin D biosynthetic process negative regulation of hormone biosynthetic process regulation of small molecule metabolic process small molecule metabolic process regulation of calcidiol 1-monooxygenase activity regulation of biological quality regulation of vitamin metabolic process hormone biosynthetic process negative regulation of monooxygenase activity negative regulation of steroid metabolic process regulation of alcohol biosynthetic process regulation of hormone levels negative regulation of oxidoreductase activity negative regulation of metabolic process cellular metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process negative regulation of vitamin metabolic process regulation of molecular function biosynthetic process negative regulation of alcohol biosynthetic process negative regulation of lipid metabolic process negative regulation of hormone metabolic process regulation of steroid biosynthetic process cellular biosynthetic process regulation of hormone metabolic process organic hydroxy compound metabolic process steroid metabolic process lipid biosynthetic process alcohol metabolic process negative regulation of cellular process steroid biosynthetic process regulation of biosynthetic process small molecule biosynthetic process regulation of steroid metabolic process negative regulation of molecular function regulation of oxidoreductase activity vitamin D metabolic process regulation of vitamin D biosynthetic process hormone metabolic process vitamin metabolic process regulation of cellular biosynthetic process regulation of monooxygenase activity negative regulation of biosynthetic process organic hydroxy compound biosynthetic process fat-soluble vitamin biosynthetic process alcohol biosynthetic process negative regulation of steroid biosynthetic process regulation of lipid biosynthetic process negative regulation of vitamin D biosynthetic process lipid metabolic process regulation of protein metabolic process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process response to interleukin-6 cellular response to interleukin-6 JNK cascade MAPK cascade negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process cellular response to interleukin-1 response to interleukin-1 mucopolysaccharide metabolic process glycosaminoglycan metabolic process regulation of hyaluronan biosynthetic process carbohydrate derivative metabolic process regulation of polysaccharide metabolic process hyaluronan metabolic process polysaccharide metabolic process positive regulation of hyaluronan biosynthetic process glycosaminoglycan biosynthetic process regulation of carbohydrate metabolic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process hyaluronan biosynthetic process regulation of polysaccharide biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process canonical NF-kappaB signal transduction immune response-regulating cell surface receptor 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 cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process regulation of localization lipid storage lipid localization positive regulation of lipid localization maintenance of location localization regulation of lipid storage regulation of lipid localization macromolecule localization positive regulation of lipid storage regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response negative regulation of response to stimulus regulation of inflammatory response negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response response to lipid cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus response to bacterium cellular response to lipid response to molecule of bacterial origin regulation of developmental process cellular developmental process macrophage derived foam cell differentiation regulation of cell differentiation positive regulation of developmental process foam cell differentiation positive regulation of cell differentiation cell differentiation regulation of macrophage derived foam cell differentiation positive regulation of macrophage derived foam cell differentiation cellular response to tumor necrosis factor response to tumor necrosis factor regulation of DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter positive regulation of DNA-templated transcription initiation positive regulation of transcription initiation by RNA polymerase II DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II negative regulation of sterol transport transport regulation of lipid transport negative regulation of transport organic hydroxy compound transport negative regulation of lipid localization sterol transport regulation of cholesterol transport regulation of sterol transport negative regulation of lipid transport regulation of transport negative regulation of cholesterol transport lipid transport establishment of localization cholesterol transport cellular response to nicotine response to nicotine response to mechanical stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus regulation of interleukin-12 production negative regulation of interleukin-12 production cytokine production regulation of cytokine production regulation of multicellular organismal process interleukin-12 production negative regulation of cytokine production negative regulation of gene expression negative regulation of multicellular organismal process positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway regulation of signal transduction positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of signaling regulation of Wnt signaling pathway regulation of cell communication positive regulation of signaling response to angiotensin response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus cellular response to angiotensin cellular response to endogenous stimulus response to hormone cellular response to hormone stimulus cellular response to virus response to virus response to muscle stretch antibacterial innate immune response defense response to bacterium	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex transcription regulator complex intracellular organelle organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle I-kappaB/NF-kappaB complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex transcription regulator complex intracellular organelle organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle I-kappaB/NF-kappaB complex intracellular protein-containing complex membrane-bounded organelle NF-kappaB p50/p65 complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle NF-kappaB complex vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen endomembrane system intracellular organelle lumen cytoplasmic vesicle organelle lumen specific granule lumen secretory granule secretory vesicle vesicle specific granule mitochondrion nucleoplasm nuclear lumen extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR030503	Nuclear factor NF-kappa-B, p105 subunit, Rel homology domain, N-terminal	Domain
A	IPR002909	IPT domain	Domain
A	IPR030492	Rel homology domain, conserved site	Conserved Site
A	IPR033926	NFkappaB IPT domain	Domain
A	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A	IPR002110	Ankyrin repeat	Repeat
A	IPR000488	Death domain	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR037059	Rel homology domain (RHD), DNA-binding domain superfamily	Homologous Superfamily
A	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A	IPR011539	Rel homology domain, DNA-binding domain	Domain
A	IPR011029	Death-like domain superfamily	Homologous Superfamily
A	IPR000451	NF-kappa-B/Dorsal	Family
A	IPR047096	Nuclear factor NF-kappa-B p105 subunit, death domain	Domain
A	IPR032397	Rel homology dimerisation domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P19838	common variable immunodeficiency primary biliary cholangitis tubular adenocarcinoma granular cell carcinoma immunodeficiency, common variable, 12 brain ischemia chronic kidney disease type 2 diabetes mellitus Heat Stroke adenocarcinoma liver disease malignant colon neoplasm ulcerative colitis cribriform carcinoma of breast endogenous depression common variable immunodeficiency primary biliary cholangitis tubular adenocarcinoma granular cell carcinoma immunodeficiency, common variable, 12 brain ischemia chronic kidney disease type 2 diabetes mellitus Heat Stroke adenocarcinoma liver disease malignant colon neoplasm ulcerative colitis cribriform carcinoma of breast endogenous depression leukopenia lung cancer alopecia membranous glomerulonephritis benign colon neoplasm ovarian cyst systemic sclerosis corpus luteum cyst diabetes mellitus acute kidney failure primary hyperoxaluria colonic neoplasm tuberculosis cribriform carcinoma glioblastoma allergic rhinitis maturity-onset diabetes of the young attention deficit hyperactivity disorder, inattentive type

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.