5JUL

Near atomic structure of the Dark apoptosome

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	PF00931	NB-ARC domain (NB-ARC)	NB-ARC domain	-	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	PF22164	Dark, winged-helix domain (Dark_WHD)	Dark, winged-helix domain	This entry represents a WH-like present in a set of Dark (Drosophila Apaf-1-related killer) proteins in arthropods. Dark protein is part of the apoptosome complex and plays a key role in procaspases activation and apoptosis [1,2].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	PF17908	APAF-1 helical domain (APAF1_C)	APAF-1 helical domain	This domain represents the C-terminal alpha helical domain of the apoptotic Apaf-1 protein.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	PF22080	Dark, CARD domain (Dark_CARD)	Dark, CARD domain	This entry represents a caspase recruitment domain (CARD) present in a set of Dark (Drosophila Apaf-1-related killer) proteins in arthropods. Dark protein is part of the apoptosome complex and plays a key role in procaspases activation and apoptosis ...	This entry represents a caspase recruitment domain (CARD) present in a set of Dark (Drosophila Apaf-1-related killer) proteins in arthropods. Dark protein is part of the apoptosome complex and plays a key role in procaspases activation and apoptosis [1]. This N-terminal CARD in Dark belongs to the alpha-helical Death Domain superfamily and interacts with the N-terminal CARD of Dronc protein [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	Apaf-1 related killer DARK	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 ADP binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity cysteine-type endopeptidase activator activity involved in apoptotic process molecular function regulator activity cysteine-type endopeptidase regulator activity involved in apoptotic process peptidase activator activity peptidase activator activity involved in apoptotic process CARD domain binding protein binding protein domain specific binding identical protein binding	compound eye retinal cell programmed cell death multicellular organismal process regulation of cellular process positive regulation of compound eye retinal cell programmed cell death cellular developmental process regulation of developmental process sensory organ development positive regulation of biological process visual system development cell development regulation of programmed cell death positive regulation of developmental process eye morphogenesis multicellular organism development compound eye morphogenesis compound eye retinal cell programmed cell death multicellular organismal process regulation of cellular process positive regulation of compound eye retinal cell programmed cell death cellular developmental process regulation of developmental process sensory organ development positive regulation of biological process visual system development cell development regulation of programmed cell death positive regulation of developmental process eye morphogenesis multicellular organism development compound eye morphogenesis cell differentiation regulation of retinal cell programmed cell death anatomical structure development animal organ morphogenesis sensory system development positive regulation of cellular process system development developmental process regulation of biological process positive regulation of programmed cell death eye development biological regulation animal organ development cell death positive regulation of retinal cell programmed cell death programmed cell death involved in cell development anatomical structure morphogenesis regulation of compound eye retinal cell programmed cell death compound eye development sensory organ morphogenesis retinal cell programmed cell death cellular process programmed cell death S-adenosylmethionine cycle S-adenosylmethionine metabolic process cellular metabolic process sulfur compound metabolic process metabolic process spermatid development spermatid differentiation sexual reproduction spermatogenesis reproductive process cellularization cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation multicellular organismal reproductive process sperm individualization male gamete generation anatomical structure formation involved in morphogenesis germ cell development chemical homeostasis homeostatic process triglyceride homeostasis acylglycerol homeostasis lipid homeostasis regulation of apoptotic process positive regulation of apoptotic process apoptotic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process sarcosine catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process non-proteinogenic amino acid catabolic process carboxylic acid metabolic process sarcosine metabolic process primary metabolic process cellular modified amino acid metabolic process alpha-amino acid catabolic process small molecule catabolic process cellular modified amino acid catabolic process cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cellular component organization or biogenesis plasma membrane bounded cell projection organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons neuron development pigment metabolic process melanization defense response biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response organic hydroxy compound metabolic process defense response to symbiont response to external stimulus response to biotic stimulus melanin metabolic process secondary metabolic process immune system process defense response to other organism response to stress phenol-containing compound metabolic process innate immune response response to external biotic stimulus central nervous system formation central nervous system development central nervous system morphogenesis autophagic cell death regulation of glial cell apoptotic process positive regulation of glial cell apoptotic process glial cell apoptotic process chaeta development response to ionizing radiation response to radiation response to abiotic stimulus response to gamma radiation regulation of humoral immune response humoral immune response negative regulation of response to stimulus negative regulation of immune response negative regulation of humoral immune response negative regulation of biological process regulation of response to stimulus negative regulation of immune system process regulation of immune response regulation of immune system process cellular homeostasis neuron cellular homeostasis response to nutrient levels response to starvation salivary gland histolysis gland development salivary gland development instar larval or pupal development metamorphosis anatomical structure regression gland morphogenesis instar larval or pupal morphogenesis salivary gland morphogenesis post-embryonic animal morphogenesis post-embryonic development exocrine system development	protein-containing complex intracellular anatomical structure apoptosome cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR041452	APAF-1 helical domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR002182	NB-ARC	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR001680	WD40 repeat	Repeat

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 R01GM133198.