3GD3

Crystal structure of a naturally folded murine apoptosis inducing factor

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)
C	SCOP2B Superfamily	GSR C-terminal domain-like	8056228	3000028	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thioredoxin reductase-like	8044630	3000050	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GSR C-terminal domain-like	8056228	3000028	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thioredoxin reductase-like	8044630	3000050	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GSR C-terminal domain-like	8056228	3000028	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thioredoxin reductase-like	8044630	3000050	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thioredoxin reductase-like	8044630	3000050	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GSR C-terminal domain-like	8056228	3000028	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)
C	AIF_C	e3gd3C1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: AIF_C	ECOD (1.6)
C	Pyr_redox_2_1	e3gd3C3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_1	ECOD (1.6)
C	Pyr_redox_2	e3gd3C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)
A	AIF_C	e3gd3A1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: AIF_C	ECOD (1.6)
A	Pyr_redox_2_1	e3gd3A3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_1	ECOD (1.6)
A	Pyr_redox_2	e3gd3A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)
B	AIF_C	e3gd3B1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: AIF_C	ECOD (1.6)
B	Pyr_redox_2_1	e3gd3B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_1	ECOD (1.6)
B	Pyr_redox_2	e3gd3B3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)
D	AIF_C	e3gd3D1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: AIF_C	ECOD (1.6)
D	Pyr_redox_2_1	e3gd3D3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_1	ECOD (1.6)
D	Pyr_redox_2	e3gd3D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
C	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
B	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
D	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
D	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain
A, B, C, D	PF14721	Apoptosis-inducing factor, mitochondrion-associated, C-term (AIF_C)	Apoptosis-inducing factor, mitochondrion-associated, C-term	This C-terminal domain appears to be a dimerisation domain of the mitochondrial apoptosis-inducing factor 1. protein. The domain also appears at the C-terminus of FAD-dependent pyridine nucleotide-disulfide oxidoreductases. Apoptosis inducing factor ...	This C-terminal domain appears to be a dimerisation domain of the mitochondrial apoptosis-inducing factor 1. protein. The domain also appears at the C-terminus of FAD-dependent pyridine nucleotide-disulfide oxidoreductases. Apoptosis inducing factor (AIF) is a bifunctional mitochondrial flavoprotein critical for energy metabolism and induction of caspase-independent apoptosis. On reduction with NADH, AIF undergoes dimerisation and forms tight, long-lived FADH2-NAD charge-transfer complexes proposed to be functionally important.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Apoptosis-inducing factor 1, mitochondrial	FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity electron transfer activity oxidoreductase activity, acting on the CH-NH group of donors electron-transferring-flavoprotein dehydrogenase activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity electron transfer activity oxidoreductase activity, acting on the CH-NH group of donors electron-transferring-flavoprotein dehydrogenase activity catalytic activity oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor NAD(P)H oxidase H2O2-forming activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor DNA binding nucleic acid binding NADH dehydrogenase activity poly-ADP-D-ribose binding carbohydrate derivative binding protein binding protein dimerization activity	cellular component organization organelle organization apoptotic mitochondrial changes cellular process apoptotic process cellular component organization or biogenesis cell death programmed cell death mitochondrion organization regulation of catalytic activity positive regulation of protein metabolic process positive regulation of peptidase activity positive regulation of biological process positive regulation of cysteine-type endopeptidase activity involved in apoptotic process cellular component organization organelle organization apoptotic mitochondrial changes cellular process apoptotic process cellular component organization or biogenesis cell death programmed cell death mitochondrion organization regulation of catalytic activity positive regulation of protein metabolic process positive regulation of peptidase activity positive regulation of biological process positive regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of primary metabolic process positive regulation of molecular function positive regulation of metabolic process regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of proteolysis proteolysis regulation of endopeptidase activity positive regulation of macromolecule metabolic process protein metabolic process activation of cysteine-type endopeptidase activity involved in apoptotic process regulation of cysteine-type endopeptidase activity regulation of biological process regulation of protein metabolic process regulation of peptidase activity biological regulation positive regulation of catalytic activity primary metabolic process regulation of macromolecule metabolic process regulation of molecular function positive regulation of hydrolase activity positive regulation of cysteine-type endopeptidase activity regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis metabolic process macromolecule metabolic process regulation of metabolic process response to stimulus response to stress response to ischemia response to decreased oxygen levels cellular response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to chemical response to oxygen levels response to abiotic stimulus response to ketone response to lipid cellular response to mineralocorticoid stimulus response to mineralocorticoid cellular response to endogenous stimulus cellular response to aldehyde response to hormone response to steroid hormone cellular response to ketone response to organic cyclic compound cellular response to steroid hormone stimulus cellular response to hormone stimulus cellular response to aldosterone response to aldosterone response to endogenous stimulus response to alcohol cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid cellular response to alcohol cellular response to lipid positive regulation of programmed cell death regulation of cellular process regulation of apoptotic 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 response to toxic substance cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species catabolic process macromolecule catabolic process regulation of DNA catabolic process nucleobase-containing compound metabolic process execution phase of apoptosis DNA catabolic process apoptotic nuclear changes regulation of nucleobase-containing compound metabolic process regulation of apoptotic DNA fragmentation cellular component disassembly DNA 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 regulation of DNA metabolic process signaling intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress intracellular signal transduction cell communication apoptotic signaling pathway signal transduction intrinsic apoptotic signaling pathway response to endoplasmic reticulum stress response to estradiol cellular response to estradiol stimulus positive regulation of necroptotic process necroptotic process programmed necrotic cell death regulation of necroptotic process regulation of programmed necrotic cell death positive regulation of programmed necrotic cell death response to acid chemical response to nitrogen compound response to L-glutamate response to amino acid cellular component biogenesis cellular component assembly mitochondrial respiratory chain complex assembly protein-containing complex organization protein-containing complex assembly protein localization establishment of protein localization cellular localization nitrogen compound transport protein transmembrane import into intracellular organelle transport protein targeting localization protein transmembrane transport cellular macromolecule localization mitochondrial transport protein import into mitochondrial intermembrane space establishment of localization mitochondrial transmembrane transport transmembrane transport establishment of protein localization to organelle protein transport macromolecule localization protein localization to organelle protein localization to mitochondrion protein targeting to mitochondrion establishment of protein localization to mitochondrion cellular response to nitrogen compound cellular response to nitric oxide response to nitric oxide cellular response to reactive nitrogen species	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane cytosol perinuclear region of cytoplasm organelle outer membrane bounding membrane of organelle mitochondrial outer membrane outer membrane mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle lumen nucleus
E, F	Apoptosis-inducing factor 1, mitochondrial	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029324	Mitochondrial apoptosis-inducing factor, C-terminal domain	Domain
A, B, C, D	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily	Homologous Superfamily
A, B, C, D	IPR050446	FAD-dependent Oxidoreductases and Apoptosis Regulators	Family
A, B, C, D	IPR023753	FAD/NAD(P)-binding 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.