4M9S | pdb_00004m9s

crystal structure of CED-4 bound CED-3 fragment

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DEATH domain	8003077	3000069	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	DEATH domain	8003077	3000069	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	DEATH domain	8003077	3000069	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003079	3000034	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104155	3002834	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8003074	3002019	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	DEATH domain	8003077	3000069	SCOP2B (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		e4m9sA2	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: His_biosynth	F:	ECOD (20:10:01)
A		e4m9sA4	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Flav_NS3-hel_C	F:	ECOD (20:10:01)
G [auth D]		e4m9sD2	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: His_biosynth	F:	ECOD (20:10:01)
G [auth D]		e4m9sD4	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Flav_NS3-hel_C	F:	ECOD (20:10:01)
E [auth C]		e4m9sC2	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: His_biosynth	F:	ECOD (20:10:01)
E [auth C]		e4m9sC4	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Flav_NS3-hel_C	F:	ECOD (20:10:01)
C [auth B]		e4m9sB2	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: His_biosynth	F:	ECOD (20:10:01)
C [auth B]		e4m9sB4	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Flav_NS3-hel_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)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.8.490	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
G [auth D]	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
G [auth D]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G [auth D]	1.10.8.490	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
G [auth D]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E [auth C]	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
E [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E [auth C]	1.10.8.490	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E [auth C]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C [auth B]	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
C [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C [auth B]	1.10.8.490	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C [auth B]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth C], G [auth D]	PF00931	NB-ARC domain (NB-ARC)	NB-ARC domain		Domain
A, C [auth B], E [auth C], G [auth D]	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
A, C [auth B], E [auth C], G [auth D]	PF22094	CED4, winged-helix domain (WHD_CED4)	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 dur ...	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
B [auth E], D [auth F], F [auth G], H	CED-3 fragment	-	-	-
A, C [auth B], E [auth C], G [auth D]	Cell death protein 4	cysteine-type endopeptidase activator activity endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity endopeptidase regulator activity protein binding binding BH1 domain binding BH domain binding protein domain specific binding cysteine-type endopeptidase activator activity endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity endopeptidase regulator activity 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 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 cysteine-type endopeptidase activator activity involved in apoptotic process cysteine-type endopeptidase regulator activity involved in apoptotic process peptidase activator activity involved in apoptotic process 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 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 protein metabolic process positive regulation of macromolecule biosynthetic process positive regulation of protein processing protein maturation regulation of primary metabolic process positive regulation of metabolic process regulation of proteolysis positive regulation of biosynthetic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process regulation of biosynthetic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of proteolysis regulation of protein processing protein processing metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic 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 response to bacterium response to stress 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane protein-containing complex catalytic complex caspase complex peptidase complex endopeptidase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm 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, C [auth B], E [auth C], G [auth D]	IPR002182	NB-ARC	Domain
A, C [auth B], E [auth C], G [auth D]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR054317	CED4, winged-helix domain	Domain
A, C [auth B], E [auth C], G [auth D]	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.