8JO0

The Cryo-EM structure of a heptameric CED-4/CED-3 catalytic complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth H]	SCOP2B Superfamily	DEATH domain	8003077	3000069	SCOP2B (2022-06-29)
B [auth I]	SCOP2B Superfamily	DEATH domain	8003077	3000069	SCOP2B (2022-06-29)
C [auth J]	SCOP2B Superfamily	DEATH domain	8003077	3000069	SCOP2B (2022-06-29)
D [auth K]	SCOP2B Superfamily	DEATH domain	8003077	3000069	SCOP2B (2022-06-29)
E [auth L]	SCOP2B Superfamily	DEATH domain	8003077	3000069	SCOP2B (2022-06-29)
F [auth M]	SCOP2B Superfamily	DEATH domain	8003077	3000069	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
J [auth D]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)
J [auth D]	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
J [auth D]	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)
L [auth F]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)
L [auth F]	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
L [auth F]	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
M [auth G]	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
M [auth G]	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
M [auth G]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M]	PF00619	Caspase recruitment domain (CARD)	Caspase recruitment domain	Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (Pfam:PF00531) domain-like fold .	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F], M [auth G]	PF00931	NB-ARC domain (NB-ARC)	NB-ARC domain	-	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F], M [auth G]	PF22094	CED4, winged-helix domain (CED4_WHD)	CED4, winged-helix domain	This entry represents a WH-like (HTH superfamily) domain present in CED4 proteins from nematodes. CDE4 together with EGL1, CED9, and CED3, forms a crucial component of the apoptotic signaling cascade necessary for triggering programmed cell death du ...	This entry represents a WH-like (HTH superfamily) domain present in CED4 proteins from nematodes. CDE4 together with EGL1, CED9, and CED3, forms a crucial component of the apoptotic signaling cascade necessary for triggering programmed cell death during both embryonic and postembryonic development [1,2]. Molecular dynamics studies indicate that this WH domain may regulate CED4 dissociation from CED9 [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M]	Cell death protein 4	protein binding binding BH1 domain binding BH domain binding protein domain specific binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding protein binding binding BH1 domain binding BH domain binding protein domain specific binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ADP binding death domain binding BH3 domain binding enzyme binding protease binding caspase 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 endopeptidase activator activity endopeptidase regulator activity identical protein binding	cellular component disassembly regulation of synapse pruning regulation of biological process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization cell junction disassembly synapse pruning biological regulation positive regulation of biological process positive regulation of synapse pruning cellular component organization regulation of synapse organization cell junction organization cellular component disassembly regulation of synapse pruning regulation of biological process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization cell junction disassembly synapse pruning biological regulation positive regulation of biological process positive regulation of synapse pruning cellular component organization regulation of synapse organization cell junction organization cellular process regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of biological quality positive regulation of cellular process cell adhesion regulation of cell adhesion apoptotic process involved in development developmental process anatomical structure development apoptotic process cell death programmed cell death activation of cysteine-type endopeptidase activity regulation of catalytic activity cellular biosynthetic process positive regulation of protein metabolic process positive regulation of peptidase activity protein maturation regulation of primary metabolic process positive regulation of molecular function positive regulation of metabolic process regulation of proteolysis proteolysis regulation of endopeptidase activity positive regulation of macromolecule metabolic process protein metabolic process zymogen activation regulation of cysteine-type endopeptidase activity organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process regulation of peptidase activity positive regulation of catalytic activity primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of molecular function positive regulation of hydrolase activity biosynthetic process positive regulation of cysteine-type endopeptidase activity regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis protein processing metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of cysteine-type endopeptidase activity involved in apoptotic process activation of cysteine-type endopeptidase activity involved in apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process regulation of cellular component size regulation of cell size regulation of anatomical structure size positive regulation of programmed cell death positive regulation of apoptotic process actin polymerization or depolymerization actin cytoskeleton organization protein-containing complex organization actin filament organization protein-containing complex disassembly actin filament depolymerization organelle organization actin filament-based process supramolecular fiber organization protein depolymerization cytoskeleton organization regulation of developmental process positive regulation of apoptotic process involved in development regulation of apoptotic process involved in development positive regulation of developmental process regulation of protein maturation positive regulation of protein maturation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of protein processing positive regulation of biosynthetic process regulation of biosynthetic process regulation of cellular metabolic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of protein processing regulation of macromolecule biosynthetic process positive regulation of cellular biosynthetic process negative regulation of execution phase of apoptosis regulation of execution phase of apoptosis execution phase of apoptosis multicellular organism development multicellular organismal process anatomical structure morphogenesis embryonic morphogenesis embryo development regulation of protein stability biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus regulation of development, heterochronic embryo development ending in birth or egg hatching cellular homeostasis homeostatic process muscle cell cellular homeostasis	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane protein-containing complex catalytic complex caspase complex peptidase complex endopeptidase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane protein-containing complex catalytic complex caspase complex peptidase complex endopeptidase complex cytosol perinuclear region of cytoplasm nucleus
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F], M [auth G]	Cell death protein 4	protein binding binding BH1 domain binding BH domain binding protein domain specific binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding protein binding binding BH1 domain binding BH domain binding protein domain specific binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ADP binding death domain binding BH3 domain binding enzyme binding protease binding caspase 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 endopeptidase activator activity endopeptidase regulator activity identical protein binding	cellular component disassembly regulation of synapse pruning regulation of biological process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization cell junction disassembly synapse pruning biological regulation positive regulation of biological process positive regulation of synapse pruning cellular component organization regulation of synapse organization cell junction organization cellular component disassembly regulation of synapse pruning regulation of biological process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization cell junction disassembly synapse pruning biological regulation positive regulation of biological process positive regulation of synapse pruning cellular component organization regulation of synapse organization cell junction organization cellular process regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of biological quality positive regulation of cellular process cell adhesion regulation of cell adhesion apoptotic process involved in development developmental process anatomical structure development apoptotic process cell death programmed cell death activation of cysteine-type endopeptidase activity regulation of catalytic activity cellular biosynthetic process positive regulation of protein metabolic process positive regulation of peptidase activity protein maturation regulation of primary metabolic process positive regulation of molecular function positive regulation of metabolic process regulation of proteolysis proteolysis regulation of endopeptidase activity positive regulation of macromolecule metabolic process protein metabolic process zymogen activation regulation of cysteine-type endopeptidase activity organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process regulation of peptidase activity positive regulation of catalytic activity primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of molecular function positive regulation of hydrolase activity biosynthetic process positive regulation of cysteine-type endopeptidase activity regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis protein processing metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of cysteine-type endopeptidase activity involved in apoptotic process activation of cysteine-type endopeptidase activity involved in apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process regulation of cellular component size regulation of cell size regulation of anatomical structure size positive regulation of programmed cell death positive regulation of apoptotic process actin polymerization or depolymerization actin cytoskeleton organization protein-containing complex organization actin filament organization protein-containing complex disassembly actin filament depolymerization organelle organization actin filament-based process supramolecular fiber organization protein depolymerization cytoskeleton organization regulation of developmental process positive regulation of apoptotic process involved in development regulation of apoptotic process involved in development positive regulation of developmental process regulation of protein maturation positive regulation of protein maturation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of protein processing positive regulation of biosynthetic process regulation of biosynthetic process regulation of cellular metabolic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of protein processing regulation of macromolecule biosynthetic process positive regulation of cellular biosynthetic process negative regulation of execution phase of apoptosis regulation of execution phase of apoptosis execution phase of apoptosis multicellular organism development multicellular organismal process anatomical structure morphogenesis embryonic morphogenesis embryo development regulation of protein stability biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus regulation of development, heterochronic embryo development ending in birth or egg hatching cellular homeostasis homeostatic process muscle cell cellular homeostasis	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane protein-containing complex catalytic complex caspase complex peptidase complex endopeptidase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane protein-containing complex catalytic complex caspase complex peptidase complex endopeptidase complex cytosol perinuclear region of cytoplasm nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M]	IPR002182	NB-ARC	Domain
A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M]	IPR011029	Death-like domain superfamily	Homologous Superfamily
A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M]	IPR016854	Cell death protein 4	Family
A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M]	IPR001315	CARD domain	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F], M [auth G]	IPR002182	NB-ARC	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F], M [auth G]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F], M [auth G]	IPR011029	Death-like domain superfamily	Homologous Superfamily
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F], M [auth G]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F], M [auth G]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F], M [auth G]	IPR016854	Cell death protein 4	Family
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F], M [auth G]	IPR001315	CARD domain	Domain

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.

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8JO0

The Cryo-EM structure of a heptameric CED-4/CED-3 catalytic complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage