4RHW | pdb_00004rhw

Crystal structure of Apaf-1 CARD and caspase-9 CARD complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4rhwa_	All alpha proteins	DEATH domain	DEATH domain	Caspase recruitment domain, CARD	Apoptotic protease activating factor 1, APAF-1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4rhwb_	All alpha proteins	DEATH domain	DEATH domain	Caspase recruitment domain, CARD	Apoptotic protease activating factor 1, APAF-1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4rhwc_	All alpha proteins	DEATH domain	DEATH domain	Caspase recruitment domain, CARD	Apoptotic protease activating factor 1, APAF-1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4rhwd_	All alpha proteins	DEATH domain	DEATH domain	Caspase recruitment domain, CARD	Apoptotic protease activating factor 1, APAF-1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4rhwe_	All alpha proteins	DEATH domain	DEATH domain	Caspase recruitment domain, CARD	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d4rhwf_	All alpha proteins	DEATH domain	DEATH domain	Caspase recruitment domain, CARD	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DEATH domain	8037979	3000069	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DEATH domain	8037979	3000069	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DEATH domain	8037979	3000069	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DEATH domain	8037979	3000069	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DEATH domain	8037989	3000069	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DEATH domain	8037989	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	CARD	e4rhwA1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
B	CARD	e4rhwB1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
C	CARD	e4rhwC1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
D	CARD	e4rhwD1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
E	CARD	e4rhwE1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
F	CARD	e4rhwF1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)

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)
B	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
C	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
D	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
E	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
F	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, 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
E, F	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Apoptotic protease-activating factor 1	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding 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 binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding 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 enzyme regulator activity peptidase activity peptidase regulator activity catalytic activity, acting on a protein molecular function activator activity cysteine-type endopeptidase activator activity involved in apoptotic process hydrolase activity peptidase activator activity enzyme activator activity molecular function regulator activity cysteine-type endopeptidase regulator activity involved in apoptotic process catalytic activity peptidase activator activity involved in apoptotic process identical protein binding	developmental process cellular developmental process cell differentiation cellular process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway developmental process cellular developmental process cell differentiation cellular process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process biological regulation cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death positive regulation of signaling regulation of apoptotic signaling pathway intracellular signal transduction intrinsic apoptotic signaling pathway 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 multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure head development forebrain development animal organ development brain development central nervous system development catabolic process macromolecule catabolic process regulation of DNA catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component organization execution phase of apoptosis DNA catabolic process apoptotic nuclear changes cellular component organization or biogenesis regulation of nucleobase-containing compound metabolic process regulation of apoptotic DNA fragmentation cellular component disassembly primary metabolic process DNA metabolic process regulation of macromolecule metabolic process regulation of catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process apoptotic DNA fragmentation cellular component disassembly involved in execution phase of apoptosis nucleic acid catabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic 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 neuron apoptotic process 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 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 extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space 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
E, F	Caspase-9	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity SH3 domain binding protein binding binding protein domain specific binding enzyme regulator activity enzyme activator activity molecular function activator activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity SH3 domain binding protein binding binding protein domain specific binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity kinase binding enzyme binding protein kinase binding identical protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process leukocyte apoptotic process apoptotic process cell death programmed cell death regulation of biological process regulation of cellular process signaling biological regulation cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process leukocyte apoptotic process apoptotic process cell death programmed cell death regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication signal transduction in response to DNA damage signal transduction apoptotic signaling pathway intrinsic apoptotic signaling pathway response to ischemia glial cell apoptotic process epithelial cell apoptotic process 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 neuron apoptotic process positive regulation of neuron apoptotic process regulation of neuron apoptotic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process protein metabolic process macromolecule metabolic process response to ketone response to lipid cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to ketone cellular response to steroid hormone stimulus cellular response to hormone stimulus response to endogenous stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to glucocorticoid stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid cellular response to chemical stimulus response to chemical cellular response to lipid response to dexamethasone fibroblast apoptotic process intrinsic apoptotic signaling pathway in response to DNA damage developmental process cellular developmental process hemopoiesis platelet morphogenesis cell development cell morphogenesis anatomical structure morphogenesis myeloid cell differentiation cell differentiation platelet formation anatomical structure development anatomical structure formation involved in morphogenesis response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV response to decreased oxygen levels response to hypoxia response to oxygen levels multicellular organism development multicellular organismal process animal organ development kidney development renal system development system development response to cobalt ion response to metal ion biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin response to estradiol	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex caspase complex peptidase complex endopeptidase complex cytosol membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex caspase complex peptidase complex endopeptidase complex cytosol apoptosome nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR041452	APAF-1 helical domain	Domain
A, B, C, D	IPR019775	WD40 repeat, conserved site	Conserved Site
A, B, C, D	IPR037963	Apoptotic Protease-Activating Factor 1, CARD domain	Domain
A, B, C, D	IPR002182	NB-ARC	Domain
A, B, C, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR042197	Apoptotic protease-activating factors, helical domain	Homologous Superfamily
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR048975	Apoptotic protease-activating factor 1, winged-helix domain	Domain
A, B, C, D	IPR001680	WD40 repeat	Repeat
A, B, C, D	IPR001315	CARD domain	Domain
A, B, C, D	IPR020472	G-protein beta WD-40 repeat	Repeat
A, B, C, D	IPR017251	Apoptotic protease-activating factor 1	Family
E, F	IPR001309	Peptidase C14, p20 domain	Domain
E, F	IPR011600	Peptidase C14, caspase domain	Domain
E, F	IPR016129	Peptidase family C14A, His active site	Active Site
E, F	IPR042147	CASP9, CARD domain	Domain
E, F	IPR015917	Peptidase C14A, caspase catalytic domain	Domain
E, F	IPR011029	Death-like domain superfamily	Homologous Superfamily
E, F	IPR029030	Caspase-like domain superfamily	Homologous Superfamily
E, F	IPR033139	Peptidase family C14A, cysteine active site	Active Site
E, F	IPR002138	Peptidase C14, caspase non-catalytic subunit p10	Domain
E, F	IPR001315	CARD domain	Domain
E, F	IPR002398	Peptidase C14 family	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: 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
E, F	Pharos: P55211	retinal detachment transient ischemic attack brain ischemia peripheral nervous system disease prostate cancer Edema peripheral neuropathy nervous system disorder tuberculosis adrenal cortex carcinoma cancer intestinal disease lymphatic system disease alcoholic pancreatitis liver disease retinal detachment transient ischemic attack brain ischemia peripheral nervous system disease prostate cancer Edema peripheral neuropathy nervous system disorder tuberculosis adrenal cortex carcinoma cancer intestinal disease lymphatic system disease alcoholic pancreatitis liver disease breast disease hematologic disease lung disease