Annotations: 3JBT

Atomic structure of the Apaf-1 apoptosome

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)
N	SCOP2B Superfamily	Cytochrome c	8036431	3000815	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Cytochrome c	8036431	3000815	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Cytochrome c	8036431	3000815	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Cytochrome c	8036431	3000815	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cytochrome c	8036431	3000815	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytochrome c	8036431	3000815	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochrome c	8036431	3000815	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)
N	TPR_8, TPR_19	e3jbtN1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
L	TPR_8, TPR_19	e3jbtL1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
J	TPR_8, TPR_19	e3jbtJ1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
H	TPR_8, TPR_19	e3jbtH1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
F	TPR_8, TPR_19	e3jbtF1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
D	TPR_8, TPR_19	e3jbtD1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
B	TPR_8, TPR_19	e3jbtB1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
M	TPR_8, TPR_19	e3jbtM3	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
M	WD40, Beta-prop_NOL10_N	e3jbtM7	A: alpha arrays	X: P-loop domains-like	H: Cas7-related	T: CRISPR-associated protein Cas7f/Csy3	F: WD40, Beta-prop_NOL10_N	ECOD (v295.2)
K	TPR_8, TPR_19	e3jbtK2	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
K	WD40, Beta-prop_NOL10_N	e3jbtK6	A: alpha arrays	X: P-loop domains-like	H: Cas7-related	T: CRISPR-associated protein Cas7f/Csy3	F: WD40, Beta-prop_NOL10_N	ECOD (v295.2)
I	TPR_8, TPR_19	e3jbtI1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
I	WD40, Beta-prop_NOL10_N	e3jbtI7	A: alpha arrays	X: P-loop domains-like	H: Cas7-related	T: CRISPR-associated protein Cas7f/Csy3	F: WD40, Beta-prop_NOL10_N	ECOD (v295.2)
G	TPR_8, TPR_19	e3jbtG2	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
G	WD40, Beta-prop_NOL10_N	e3jbtG6	A: alpha arrays	X: P-loop domains-like	H: Cas7-related	T: CRISPR-associated protein Cas7f/Csy3	F: WD40, Beta-prop_NOL10_N	ECOD (v295.2)
E	TPR_8, TPR_19	e3jbtE2	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
E	WD40, Beta-prop_NOL10_N	e3jbtE7	A: alpha arrays	X: P-loop domains-like	H: Cas7-related	T: CRISPR-associated protein Cas7f/Csy3	F: WD40, Beta-prop_NOL10_N	ECOD (v295.2)
C	TPR_8, TPR_19	e3jbtC1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
C	WD40, Beta-prop_NOL10_N	e3jbtC5	A: alpha arrays	X: P-loop domains-like	H: Cas7-related	T: CRISPR-associated protein Cas7f/Csy3	F: WD40, Beta-prop_NOL10_N	ECOD (v295.2)
A	TPR_8, TPR_19	e3jbtA1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: TPR_8, TPR_19	ECOD (v295.2)
A	WD40, Beta-prop_NOL10_N	e3jbtA6	A: alpha arrays	X: P-loop domains-like	H: Cas7-related	T: CRISPR-associated protein Cas7f/Csy3	F: WD40, Beta-prop_NOL10_N	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
L	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
J	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
H	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
F	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
D	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
B	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
M	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
M	1.10.8.430	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
M	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)
M	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
M	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
K	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
K	1.10.8.430	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
K	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)
K	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
K	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
I	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
I	1.10.8.430	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
I	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)
I	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
I	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
G	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	1.10.8.430	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
G	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	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
G	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	1.10.8.430	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E	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	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
E	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.10.8.430	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
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	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	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	1.10.8.430	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)
A	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L, N	PF00034	Cytochrome c (Cytochrom_C)	Cytochrome c	The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, Pfam:PF06181, has now been merged into this family.	Domain
A, C, E, G, I A, C, E, G, I, K, M	PF00931	NB-ARC domain (NB-ARC)	NB-ARC domain		Domain
A, C, E, G, I A, C, E, G, I, K, M	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, C, E, G, I A, C, E, G, I, K, M	PF21296	Apoptotic protease-activating factor 1-like, winged-helix domain (WHD_APAF1)	Apoptotic protease-activating factor 1-like, winged-helix domain	This domain is found in Apoptotic protease-activating factor 1 from Mus musculus (APAF-1), responsible to ignite the downstream cascade of caspases in the mitochondrial pathway of apoptosis. This entry represents the winged-helix domain (WHD) [1-5]. ...	This domain is found in Apoptotic protease-activating factor 1 from Mus musculus (APAF-1), responsible to ignite the downstream cascade of caspases in the mitochondrial pathway of apoptosis. This entry represents the winged-helix domain (WHD) [1-5].	Domain
A, C, E, G, I A, C, E, G, I, K, M	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L, N	Cytochrome c	binding lipid binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding	aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, cytochrome c to oxygen respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport mitochondrial electron transport, ubiquinol to cytochrome c aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, cytochrome c to oxygen respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport mitochondrial electron transport, ubiquinol to cytochrome c cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell death cell communication apoptotic signaling pathway signal transduction apoptotic process programmed cell death	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial intermembrane space mitochondrion membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle envelope lumen intracellular organelle organelle envelope organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial intermembrane space mitochondrion membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle envelope lumen intracellular organelle organelle envelope organelle lumen organelle mitochondrial envelope protein-containing complex cytochrome complex catalytic complex
A, C, E, G, I A, C, E, G, I, K, M	Apoptotic protease-activating factor 1	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule 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 binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule 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 heat shock protein binding adenyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding carbohydrate derivative binding ribonucleotide binding ADP 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	developmental process cellular developmental process cell differentiation cellular process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell death intracellular signal transduction cell communication apoptotic signaling pathway developmental process cellular developmental process cell differentiation cellular process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell death intracellular signal transduction cell communication apoptotic signaling pathway signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death cellular response to endogenous stimulus cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to endogenous stimulus response to growth factor positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular process response to G1 DNA damage checkpoint signaling response to mitotic cell cycle checkpoint signaling response to biotic stimulus cellular response to biotic stimulus response to DNA integrity checkpoint signaling response to DNA damage checkpoint signaling response to cell cycle checkpoint signaling multicellular organism development multicellular organismal process anatomical structure development nervous system development animal gross anatomical part developmental process system development response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress cellular response to stress response to endoplasmic reticulum stress response to nutrient levels response to chemical response to nutrient animal organ development kidney development renal system development muscle cell apoptotic process striated muscle cell apoptotic process cardiac muscle cell apoptotic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen intracellular vesicle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle protein-containing complex apoptosome vesicle lumen cytoplasmic vesicle lumen secretory granule lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L, N	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N	IPR009056	Cytochrome c-like domain	Domain
B, D, F, H, J B, D, F, H, J, L, N	IPR002327	Cytochrome c, class IA/ IB	Family
A, C, E, G, I A, C, E, G, I, K, M	IPR041452	APAF-1 helical domain	Domain
A, C, E, G, I A, C, E, G, I, K, M	IPR019775	WD40 repeat, conserved site	Conserved Site
A, C, E, G, I A, C, E, G, I, K, M	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
A, C, E, G, I A, C, E, G, I, K, M	IPR037963	Apoptotic Protease-Activating Factor 1, CARD domain	Domain
A, C, E, G, I A, C, E, G, I, K, M	IPR002182	NB-ARC	Domain
A, C, E, G, I A, C, E, G, I, K, M	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M	IPR042197	Apoptotic protease-activating factors, helical domain	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M	IPR048975	Apoptotic protease-activating factor 1, winged-helix domain	Domain
A, C, E, G, I A, C, E, G, I, K, M	IPR001680	WD40 repeat	Repeat
A, C, E, G, I A, C, E, G, I, K, M	IPR056153	IFT122/SMU1, beta-propeller domain	Domain
A, C, E, G, I A, C, E, G, I, K, M	IPR001315	CARD domain	Domain
A, C, E, G, I A, C, E, G, I, K, M	IPR017251	Apoptotic protease-activating factor 1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K, M	: O14727	transitional cell carcinoma renal cell carcinoma retinal detachment Skin Abnormalities collecting duct carcinoma sarcomatoid renal cell carcinoma chromophobe renal cell carcinoma papillary renal cell carcinoma adrenal cortex carcinoma clear cell renal carcinoma hepatocellular carcinoma malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm renal carcinoma cancer transitional cell carcinoma renal cell carcinoma retinal detachment Skin Abnormalities collecting duct carcinoma sarcomatoid renal cell carcinoma chromophobe renal cell carcinoma papillary renal cell carcinoma adrenal cortex carcinoma clear cell renal carcinoma hepatocellular carcinoma malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm renal carcinoma cancer exocrine pancreatic carcinoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia major depressive disorder osteosarcoma