3J9L | pdb_00003j9l

Structure of Dark apoptosome from Drosophila melanogaster

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
P [auth Q]	DNA_pol_B	e3j9lQ3	A: alpha arrays	X: OB-fold	H: Rubredoxin-related	T: Rubredoxin-related	F: DNA_pol_B	ECOD (v295.2)
O [auth P]	PCI	e3j9lP3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
O [auth P]	SHQ1-like_CS	e3j9lP1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
N [auth O]	PCI	e3j9lO3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
N [auth O]	SHQ1-like_CS	e3j9lO1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
M [auth N]	PCI	e3j9lN3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
M [auth N]	SHQ1-like_CS	e3j9lN1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
L [auth M]	PCI	e3j9lM3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
L [auth M]	SHQ1-like_CS	e3j9lM1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
K [auth L]	PCI	e3j9lL3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
K [auth L]	SHQ1-like_CS	e3j9lL1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
J [auth K]	PCI	e3j9lK3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
J [auth K]	SHQ1-like_CS	e3j9lK1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
I [auth J]	PCI	e3j9lJ3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
I [auth J]	SHQ1-like_CS	e3j9lJ1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
H [auth I]	PCI	e3j9lI3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
H [auth I]	SHQ1-like_CS	e3j9lI1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
G [auth H]	PCI	e3j9lH3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
G [auth H]	SHQ1-like_CS	e3j9lH1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
F [auth G]	PCI	e3j9lG3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
F [auth G]	SHQ1-like_CS	e3j9lG1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
E [auth F]	PCI	e3j9lF3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
E [auth F]	SHQ1-like_CS	e3j9lF1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
D [auth E]	PCI	e3j9lE3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
D [auth E]	SHQ1-like_CS	e3j9lE1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
C [auth D]	PCI	e3j9lD3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
C [auth D]	SHQ1-like_CS	e3j9lD1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
B [auth C]	PCI	e3j9lC3	A: alpha arrays	X: Cytidine deaminase-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PCI	ECOD (v295.2)
B [auth C]	SHQ1-like_CS	e3j9lC1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)
A	DNA_pol_B	e3j9lA3	A: alpha arrays	X: OB-fold	H: Rubredoxin-related	T: Rubredoxin-related	F: DNA_pol_B	ECOD (v295.2)
A	SHQ1-like_CS	e3j9lA1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: SHQ1-like_CS	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	PF00931	NB-ARC domain (NB-ARC)	NB-ARC domain		Domain
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	PF22164	Dark, winged-helix domain (WHD_Dark)	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 [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	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 [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	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 [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	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 anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ADP binding structural molecule activity CARD domain binding protein binding protein domain specific binding identical protein binding	oxoacid metabolic process sulfur amino acid metabolic process carbohydrate derivative metabolic process amino acid metabolic process L-methionine metabolic process nucleobase-containing compound metabolic process non-proteinogenic amino acid metabolic process nucleobase-containing small molecule metabolic process S-adenosylmethionine metabolic process small molecule metabolic process sulfur compound metabolic process purine ribonucleoside metabolic process homocysteine metabolic process L-methionine cycle oxoacid metabolic process sulfur amino acid metabolic process carbohydrate derivative metabolic process amino acid metabolic process L-methionine metabolic process nucleobase-containing compound metabolic process non-proteinogenic amino acid metabolic process nucleobase-containing small molecule metabolic process S-adenosylmethionine metabolic process small molecule metabolic process sulfur compound metabolic process purine ribonucleoside metabolic process homocysteine metabolic process L-methionine cycle modified amino acid metabolic process carboxylic acid metabolic process primary metabolic process nucleoside metabolic process purine-containing compound metabolic process proteinogenic amino acid metabolic process metabolic process cellular process purine nucleoside metabolic process ribonucleoside metabolic process spermatid development multicellular organismal process spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process cellularization cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation multicellular organism development cell differentiation anatomical structure development developmental process multicellular organismal reproductive process sperm individualization male gamete generation anatomical structure morphogenesis anatomical structure formation involved in morphogenesis germ cell development chemical homeostasis homeostatic process triglyceride homeostasis acylglycerol homeostasis lipid homeostasis apoptotic process cell death programmed cell death regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of developmental process positive regulation of apoptotic process involved in development regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death regulation of apoptotic process involved in development positive regulation of apoptotic process positive regulation of developmental process apoptotic process involved in development positive regulation of cellular 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 system development plasma membrane bounded cell projection organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons neuron development animal gross anatomical part developmental process 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 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 sensory organ development animal organ 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 compound eye retinal cell programmed cell death visual system development eye morphogenesis compound eye morphogenesis animal organ morphogenesis sensory system development eye development programmed cell death involved in cell development compound eye development sensory organ morphogenesis retinal cell programmed cell death 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 cellular anatomical structure intracellular anatomical structure apoptosome cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	IPR054042	Dark, winged-helix domain	Domain
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	IPR041452	APAF-1 helical domain	Domain
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	IPR054304	Dark, CARD domain	Domain
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	IPR002182	NB-ARC	Domain
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B [auth C], C [auth D], D [auth E], E [auth F], A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q]	IPR001680	WD40 repeat	Repeat

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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.