5VSM

Crystal structure of viperin with bound [4Fe-4S] cluster, 5'-deoxyadenosine, and L-methionine

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Radical_SAM_1	e5vsmA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Radical_SAM_1	ECOD (1.6)
B	Radical_SAM_1	e5vsmB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Radical_SAM_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04055	Radical SAM superfamily (Radical_SAM)	Radical SAM superfamily	Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.	Domain
A, B	PF13353	4Fe-4S single cluster domain (Fer4_12)	4Fe-4S single cluster domain	This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Radical S-adenosyl methionine domain-containing protein 2	lyase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process T-helper 2 cell cytokine production T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process type 2 immune response regulation of T-helper 2 cell cytokine production regulation of type 2 immune response cytokine production leukocyte mediated immunity positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production regulation of T cell mediated immunity regulation of cytokine production involved in immune response positive regulation of T-helper 2 cell cytokine production regulation of adaptive immune response immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity regulation of T cell cytokine production CD4-positive, alpha-beta T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process regulation of cytokine production positive regulation of immune effector process regulation of multicellular organismal process cytokine production involved in immune response positive regulation of cellular process production of molecular mediator of immune response regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process adaptive immune response positive regulation of type 2 immune response regulation of lymphocyte mediated immunity positive regulation of gene expression positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response cellular process negative regulation of protein transport protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization transport negative regulation of biological process negative regulation of transport protein localization to extracellular region localization negative regulation of secretion regulation of secretion by cell secretion by cell cellular macromolecule localization negative regulation of cellular process negative regulation of secretion by cell negative regulation of protein localization regulation of transport secretion regulation of establishment of protein localization establishment of protein localization to extracellular region negative regulation of establishment of protein localization export from cell regulation of protein transport protein secretion establishment of localization regulation of secretion regulation of protein secretion negative regulation of protein secretion protein transport regulation of cellular localization macromolecule localization cellular response to stimulus positive regulation of cell communication positive regulation of response to biotic stimulus regulation of toll-like receptor 9 signaling pathway positive regulation of signal transduction pattern recognition receptor signaling pathway regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway signal transduction innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway response to other organism regulation of innate immune response response to external stimulus positive regulation of intracellular signal transduction defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response toll-like receptor 9 signaling pathway activation of innate immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling regulation of cytoplasmic pattern recognition receptor signaling pathway endolysosomal toll-like receptor signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response response to external biotic stimulus positive regulation of toll-like receptor 9 signaling pathway regulation of signaling positive regulation of innate immune response defense response defense response to symbiont regulation of cell communication positive regulation of signaling CD4-positive, alpha-beta T cell activation T cell activation cell activation alpha-beta T cell activation lymphocyte activation leukocyte activation ossification regulation of ossification toll-like receptor 7 signaling pathway regulation of toll-like receptor 7 signaling pathway positive regulation of toll-like receptor 7 signaling pathway negative regulation of viral genome replication viral life cycle negative regulation of viral process regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication response to virus developmental process cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation CD4-positive, alpha-beta T cell differentiation alpha-beta T cell differentiation cell differentiation anatomical structure development T cell differentiation leukocyte differentiation defense response to virus	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane Golgi apparatus lipid droplet membraneless organelle intracellular membraneless organelle organelle outer membrane bounding membrane of organelle mitochondrial outer membrane outer membrane nucleus membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen fibrillar center nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007197	Radical SAM	Domain
A, B	IPR051196	RSAD2 and Viperin antiviral	Family
A, B	IPR006638	Elp3/MiaA/NifB-like, radical SAM core domain	Domain
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR026372	S-adenosylmethionine-dependent nucleotide dehydratase RSAD2	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	Viperin M-CSA #965	Viperin (Virus Inhibitory Protein, ER-associated, Iterferon-inducible) is a member of the radical S-adenosyl-l-methionine (SAM) superfamily of enzymes, which typically employ a 4Fe-4S cluster to reductively cleave SAM to initiate chemistry. It has been shown that expression of viperin causes an increase in the fluidity of lipid membranes so as to impede the budding of nascent viral particles from the membrane which inhibits the propagation of the infection. It is now known that viperin catalyses the reductive addition of a 5'-deoxyadenosyl radical to UDP-glucose in vitro.	Defined by 3 residues: CYS:A-40 [auth A-84]CYS:A-44 [auth A-88]CYS:A-47 [auth A-91] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.2 (UniProt) Search M-CSA Motif + EC 4.2

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.