1N0J

The Structure of Human Mitochondrial MN3+ Superoxide Dismutase Reveals a Novel Tetrameric Interface of Two 4-Helix Bundles

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	d1n0ja1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Mn superoxide dismutase (MnSOD)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1n0ja2	Alpha and beta proteins (a+b)	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Mn superoxide dismutase (MnSOD)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1n0jb1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Mn superoxide dismutase (MnSOD)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1n0jb2	Alpha and beta proteins (a+b)	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Mn superoxide dismutase (MnSOD)	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	Fe, Mn superoxide dismutase (SOD), C-terminal domain	8033672	3000916	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), N-terminal domain	8033670	3000794	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), C-terminal domain	8033672	3000916	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), N-terminal domain	8033670	3000794	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	Sod_Fe_N	e1n0jA4	A: alpha bundles	X: Long alpha-hairpin	H: Fe,Mn superoxide dismutase (SOD), N-terminal domain (From Topology)	T: Fe,Mn superoxide dismutase (SOD), N-terminal domain	F: Sod_Fe_N	ECOD (1.6)
A	Sod_Fe_C	e1n0jA3	A: a+b three layers	X: Fe,Mn superoxide dismutase (SOD)-C (From Topology)	H: Fe,Mn superoxide dismutase (SOD)-C (From Topology)	T: Fe,Mn superoxide dismutase (SOD)-C	F: Sod_Fe_C	ECOD (1.6)
B	Sod_Fe_N	e1n0jB4	A: alpha bundles	X: Long alpha-hairpin	H: Fe,Mn superoxide dismutase (SOD), N-terminal domain (From Topology)	T: Fe,Mn superoxide dismutase (SOD), N-terminal domain	F: Sod_Fe_N	ECOD (1.6)
B	Sod_Fe_C	e1n0jB3	A: a+b three layers	X: Fe,Mn superoxide dismutase (SOD)-C (From Topology)	H: Fe,Mn superoxide dismutase (SOD)-C (From Topology)	T: Fe,Mn superoxide dismutase (SOD)-C	F: Sod_Fe_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.287.990	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Fe,Mn superoxide dismutase (SOD) domain	CATH (4.3.0)
A	3.55.40.20	Alpha Beta	3-Layer(bab) Sandwich	minor pseudopilin epsh fold	Iron/manganese superoxide dismutase, C-terminal domain	CATH (4.3.0)
B	1.10.287.990	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Fe,Mn superoxide dismutase (SOD) domain	CATH (4.3.0)
B	3.55.40.20	Alpha Beta	3-Layer(bab) Sandwich	minor pseudopilin epsh fold	Iron/manganese superoxide dismutase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00081	Iron/manganese superoxide dismutases, alpha-hairpin domain (Sod_Fe_N)	Iron/manganese superoxide dismutases, alpha-hairpin domain	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytopla ...	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error?	Domain
A, B	PF02777	Iron/manganese superoxide dismutases, C-terminal domain (Sod_Fe_C)	Iron/manganese superoxide dismutases, C-terminal domain	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplas ...	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Superoxide dismutase [Mn]	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity oxygen binding enzyme binding	regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process biological regulation positive regulation of biological process reactive nitrogen species metabolic process positive regulation of nitric oxide metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process metabolic process regulation of nitric oxide metabolic process regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process biological regulation positive regulation of biological process reactive nitrogen species metabolic process positive regulation of nitric oxide metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process response to stimulus response to chemical response to xenobiotic stimulus response to stress response to wounding response to axon injury developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development system process circulatory system process regulation of blood pressure regulation of biological quality blood circulation response to nutrient levels response to monosaccharide response to carbohydrate response to nutrient response to oxygen-containing compound response to L-ascorbic acid response to vitamin response to organic cyclic compound multicellular organismal-level iron ion homeostasis inorganic ion homeostasis multicellular organismal-level homeostasis chemical homeostasis homeostatic process multicellular organismal-level chemical homeostasis monoatomic ion homeostasis monoatomic cation homeostasis cellular developmental process hemopoiesis cell differentiation cell development cellular process cellular homeostasis intracellular oxygen homeostasis intracellular chemical homeostasis glutathione metabolic process cellular metabolic process sulfur compound metabolic process amide metabolic process cellular modified amino acid metabolic process response to silicon dioxide cellular response to stimulus response to oxidative stress cellular response to chemical stimulus cellular response to stress cellular response to oxidative stress cellular response to chemical stress response to electrical stimulus response to abiotic stimulus positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching smooth muscle cell differentiation regulation of cellular process regulation of developmental process positive regulation of smooth muscle cell differentiation regulation of smooth muscle cell differentiation regulation of cell differentiation muscle cell differentiation muscle structure development positive regulation of developmental process regulation of cell differentiation involved in phenotypic switching vascular associated smooth muscle cell differentiation cell differentiation involved in phenotypic switching regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching positive regulation of cell differentiation positive regulation of cellular process vascular associated smooth muscle cell differentiation involved in phenotypic switching positive regulation of vascular associated smooth muscle cell differentiation positive regulation of cell differentiation involved in phenotypic switching reversible differentiation regulation of vascular associated smooth muscle cell differentiation positive regulation of muscle cell differentiation phenotypic switching vasculature development regulation of muscle cell differentiation response to metal ion response to zinc ion response to alcohol cellular response to oxygen-containing compound cellular response to alcohol cellular response to ethanol response to ethanol negative regulation of cell population proliferation fibroblast proliferation cell population proliferation negative regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of fibroblast proliferation response to decreased oxygen levels response to hypoxia response to oxygen levels reactive oxygen species biosynthetic process cellular biosynthetic process reactive oxygen species metabolic process hydrogen peroxide metabolic process hydrogen peroxide biosynthetic process response to hydrogen peroxide response to reactive oxygen species detection of stimulus detection of chemical stimulus detection of oxygen regulation of vascular associated smooth muscle cell proliferation regulation of smooth muscle cell proliferation negative regulation of vascular associated smooth muscle cell proliferation smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation regulation of tube diameter acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure regulation of systemic arterial blood pressure by neurotransmitter regulation of systemic arterial blood pressure mediated by a chemical signal nervous system process regulation of systemic arterial blood pressure by acetylcholine regulation of tube size negative regulation of blood pressure regulation of systemic arterial blood pressure negative regulation of systemic arterial blood pressure vascular process in circulatory system blood vessel diameter maintenance nervous system process involved in regulation of systemic arterial blood pressure vasodilation regulation of anatomical structure size hepaticobiliary system development gland development liver development fat cell differentiation negative regulation of developmental process negative regulation of fat cell differentiation negative regulation of cell differentiation regulation of fat cell differentiation regulation of membrane hyperpolarization membrane hyperpolarization negative regulation of membrane hyperpolarization regulation of membrane potential superoxide metabolic process superoxide anion generation behavior locomotory behavior response to manganese ion response to selenium ion response to magnetism detoxification response to superoxide cellular oxidant detoxification cellular response to oxygen radical cellular response to reactive oxygen species cellular detoxification response to toxic substance removal of superoxide radicals cellular response to superoxide cellular response to toxic substance response to oxygen radical regulation of mitochondrial membrane potential protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis response to activity neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of neuron apoptotic process pigment cell differentiation pigmentation developmental pigmentation erythrophore differentiation signaling intracellular signal transduction cell communication apoptotic signaling pathway DNA damage response intrinsic apoptotic signaling pathway in response to DNA damage signal transduction intrinsic apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to oxidative stress regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction regulation of intrinsic apoptotic signaling pathway negative regulation of cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway regulation of signaling negative regulation of response to stimulus negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of signal transduction negative regulation of intrinsic apoptotic signaling pathway regulation of response to stimulus regulation of cell communication regulation of apoptotic signaling pathway response to immobilization stress positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion response to isolation stress positive regulation of cellular metabolic process regulation of hydrogen peroxide metabolic process positive regulation of hydrogen peroxide metabolic process regulation of hydrogen peroxide biosynthetic process positive regulation of reactive oxygen species biosynthetic process regulation of cellular metabolic process positive regulation of hydrogen peroxide biosynthetic process regulation of reactive oxygen species biosynthetic process positive regulation of reactive oxygen species metabolic process regulation of cellular biosynthetic process regulation of reactive oxygen species metabolic process positive regulation of cellular biosynthetic process response to ionizing radiation response to radiation response to gamma radiation RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription positive regulation of programmed cell death muscle cell apoptotic process positive regulation of smooth muscle cell apoptotic process smooth muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of smooth muscle cell apoptotic process positive regulation of apoptotic process positive regulation of muscle cell apoptotic process vascular associated smooth muscle cell apoptotic process positive regulation of vascular associated smooth muscle cell apoptotic process regulation of vascular associated smooth muscle cell apoptotic process response to cadmium ion cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain generation of precursor metabolites and energy apoptotic mitochondrial changes release of cytochrome c from mitochondria organelle organization mitochondrion organization post-embryonic development biological process involved in interspecies interaction between organisms response to lipid 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 nervous system development generation of neurons neurogenesis neuron differentiation neuron development response to hyperoxia response to increased oxygen levels	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure mitochondrion membrane-enclosed lumen nucleoid extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure mitochondrion membrane-enclosed lumen nucleoid intracellular membrane-bounded organelle mitochondrial matrix intracellular organelle lumen intracellular organelle organelle lumen intracellular non-membrane-bounded organelle cytoplasm mitochondrial nucleoid non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001189	Manganese/iron superoxide dismutase	Family
A, B	IPR019833	Manganese/iron superoxide dismutase, binding site	Binding Site
A, B	IPR019832	Manganese/iron superoxide dismutase, C-terminal	Domain
A, B	IPR019831	Manganese/iron superoxide dismutase, N-terminal	Domain
A, B	IPR036314	Manganese/iron superoxide dismutase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR036324	Manganese/iron superoxide dismutase, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR050265	Iron/Manganese Superoxide Dismutase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P04179	psoriasis plasma cell myeloma rheumatoid arthritis squamous cell carcinoma extrinsic allergic alveolitis Farber lipogranulomatosis abdominal aortic aneurysm perinatal asphyxia MELAS syndrome amyotrophic lateral sclerosis hyperthyroidism sarcoidosis Turner syndrome diffuse large B-cell lymphoma Marfan syndrome psoriasis plasma cell myeloma rheumatoid arthritis squamous cell carcinoma extrinsic allergic alveolitis Farber lipogranulomatosis abdominal aortic aneurysm perinatal asphyxia MELAS syndrome amyotrophic lateral sclerosis hyperthyroidism sarcoidosis Turner syndrome diffuse large B-cell lymphoma Marfan syndrome renal cell carcinoma classic familial adenomatous polyposis adrenoleukodystrophy sideroblastic anemia uveitis methylmalonic acidemia esophageal squamous cell carcinoma malignant mesothelioma cardiomyopathy invasive ductal breast carcinoma nasopharyngeal carcinoma dilated cardiomyopathy Sengers syndrome nephrotic syndrome Alzheimer disease middle cerebral artery infarction Esophageal Stenosis breast cancer hypertensive disorder obesity disorder male infertility progressive external ophthalmoplegia carcinoma anemia osteoporosis aortic disease ovarian cancer sarcomatoid renal cell carcinoma autoimmune disease chromophobe renal cell carcinoma adenocarcinoma tubular adenocarcinoma papilloma peripheral neuropathy bipolar disorder collecting duct carcinoma adult acute respiratory distress syndrome head and neck squamous cell carcinoma alcoholic liver cirrhosis brain ischemia esophageal cancer non-small cell lung carcinoma esophagitis breast carcinoma prostate cancer multiple chemical sensitivity thyroid gland undifferentiated (anaplastic) carcinoma myelomeningocele pulmonary hypertension myocardial infarction interstitial lung disease transient ischemic attack atherosclerosis acute coronary syndrome perinatal necrotizing enterocolitis kidney disease skin neoplasm congestive heart failure squamous papilloma major depressive disorder exocrine pancreatic carcinoma cancer hypoglycemia malignant colon neoplasm sarcomatoid carcinoma central nervous system disease radiation injury acute kidney tubular necrosis papillary renal cell carcinoma Parkinson disease gestational diabetes type 2 diabetes mellitus peripheral nervous system disease granular cell carcinoma urinary bladder cancer colorectal cancer Lewy body dementia vascular disease visual epilepsy microvascular complications of diabetes, susceptibility to, 6 skin cancer coronary artery disease cribriform carcinoma of breast osteoarthritis malignant ependymoma myeloid neoplasm cystic fibrosis fatty liver disease interstitial cystitis depressive disorder gastric cancer pustulosis palmaris et plantaris pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ischemia reperfusion injury benign mesothelioma glioblastoma renal carcinoma kidney cancer ulcerative colitis dilated cardiomyopathy 1A urinary bladder neoplasm drug psychosis drug-induced liver injury mesothelioma Sjogren syndrome colorectal carcinoma skin disease lung carcinoma hepatocellular carcinoma malignant glioma Crohn disease osteoarthritis susceptibility 1 ovarian neoplasm gastric neoplasm schizophrenia myopathy transitional cell carcinoma pancreatic neoplasm B-cell chronic lymphocytic leukemia genetic intestinal polyposis chronic obstructive pulmonary disease necrotizing enterocolitis ischemic disease papillomatosis benign neoplasm neoplasm of esophagus undifferentiated carcinoma colonic neoplasm lung adenocarcinoma precancerous condition lung disease hereditary diffuse gastric adenocarcinoma primary ovarian failure cribriform carcinoma oral cavity neoplasm inborn mitochondrial metabolism disorder tongue cancer cutaneous lupus erythematosus arteriosclerosis disorder myocardial ischemia dermatomyositis malignant pancreatic neoplasm tuberculosis diabetic kidney disease benign colon neoplasm maturity-onset diabetes of the young clear cell renal carcinoma adrenomyeloneuropathy kidney neoplasm plasma cell neoplasm brain cancer head and neck cancer brain injury heart failure neurodegenerative disease lung cancer

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.