8XQK | pdb_00008xqk

The Crystal Structure of Apaf from Biortus.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Copine	e8xqkA01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: Copine	ECOD (v294.1)

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

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 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 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 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
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	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
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	IPR017251	Apoptotic protease-activating factor 1	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

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.