2DBF | pdb_00002dbf

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		e2dbfA1	A: Profilin-like	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: Transketolase_C	F:	ECOD (20:10:01)

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 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 DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA 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	positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process regulation of transport biological regulation lipid localization lipid transport positive regulation of lipid localization establishment of localization positive regulation of lipid transport positive regulation of transport regulation of lipid localization macromolecule localization cholesterol transport cholesterol efflux cellular response to nitrogen compound cellular response to stimulus cellular response to chemical stimulus cellular response to dsRNA response to stimulus response to chemical response to dsRNA response to nitrogen compound cellular process 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 regulation of cellular process RNA metabolic process positive regulation of miRNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process positive regulation of cellular process primary metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of RNA metabolic process metabolic process macromolecule metabolic process regulation of metabolic process signaling non-canonical NF-kappaB signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction response to interleukin-6 cellular response to interleukin-6 JNK cascade MAPK cascade cell surface receptor signaling pathway cytokine-mediated signaling pathway cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway response to tumor necrosis factor negative regulation of biological process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process 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 macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of transcription by RNA polymerase II positive regulation of RNA biosynthetic process regulation of steroid biosynthetic process negative regulation of small molecule metabolic process steroid metabolic process regulation of lipid metabolic process vitamin biosynthetic process lipid biosynthetic process negative regulation of lipid biosynthetic process vitamin D biosynthetic process regulation of small molecule metabolic process small molecule metabolic process regulation of vitamin metabolic process steroid biosynthetic process negative regulation of steroid metabolic process small molecule biosynthetic process regulation of steroid metabolic process vitamin D metabolic process regulation of vitamin D biosynthetic process vitamin metabolic process negative regulation of vitamin metabolic process fat-soluble vitamin biosynthetic process negative regulation of steroid biosynthetic process regulation of lipid biosynthetic process negative regulation of vitamin D biosynthetic process negative regulation of lipid metabolic process lipid 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 immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway regulation of response to stimulus immune system process 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 lipid storage regulation of lipid storage nutrient storage positive regulation of lipid storage regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response biological process involved in interspecies interaction between organisms response to lipid response to other organism 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 response to biotic stimulus cellular response to biotic stimulus response to bacterium cellular response to lipid response to external biotic stimulus 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 regulation of DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter positive regulation of transcription initiation by RNA polymerase II DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II 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 defense response to symbiont antibacterial innate immune response defense response to bacterium defense response to other organism innate immune response regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome I-kappaB/NF-kappaB complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.