5NT7

Structure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain of Vasa

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth B]	d5nt7b_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
D	d5nt7d_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	PF00271	e5nt7B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00271	ECOD (1.6)
D	PF00271	e5nt7D1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00271	ECOD (1.6)
B [auth A]	PF12872	e5nt7A1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF12872	ECOD (1.6)
C	PF12872	e5nt7C1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF12872	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B [auth A]	3.30.420.610	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.610	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], C	PF12872	OST-HTH/LOTUS domain (OST-HTH)	OST-HTH/LOTUS domain	A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood [1][2]. The domain adopts the ...	A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood [1][2]. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA [1].In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], D	ATP-dependent RNA helicase vasa, isoform A	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA RNA binding nucleic acid binding	developmental process cellular developmental process cell differentiation cellular process sexual reproduction reproductive process multicellular organismal reproductive process gamete generation oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation developmental process involved in reproduction anatomical structure development developmental process cellular developmental process cell differentiation cellular process sexual reproduction reproductive process multicellular organismal reproductive process gamete generation oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation developmental process involved in reproduction anatomical structure development germ cell development protein localization localization cellular localization cellular macromolecule localization macromolecule localization regulation of cellular process cellular biosynthetic process piRNA processing negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process secondary piRNA processing cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process nucleic acid metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle pole plasm intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle pole plasm intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle membrane-bounded organelle nucleus germ cell nucleus intracellular membrane-bounded organelle cell periphery cell cortex posterior cell cortex cell cortex region cytoplasmic region
B [auth A], C	Maternal effect protein oskar	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process catabolic process cellular biosynthetic process RNA metabolic process macromolecule catabolic process regulation of mRNA catabolic process organic substance metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process regulation of mRNA stability regulation of cellular biosynthetic process negative regulation of biosynthetic process regulation of RNA stability cellular process regulation of mRNA metabolic process organic substance catabolic process developmental process sexual reproduction cellular developmental process reproductive process oogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism female gamete generation developmental process involved in reproduction gamete generation cell differentiation anatomical structure development germ cell development multicellular organism development multicellular organismal process segmentation pattern specification process regionalization blastoderm segmentation anterior/posterior pattern specification anterior/posterior axis specification, embryo embryo development oocyte development tripartite regional subdivision cellular component biogenesis cellular component organization embryonic axis specification cellular component assembly anterior/posterior axis specification cellular component organization or biogenesis cell maturation embryonic pattern specification oocyte axis specification oocyte construction oocyte anterior/posterior axis specification developmental maturation cytoplasm organization pole plasm assembly anatomical structure maturation maternal determination of anterior/posterior axis, embryo oocyte differentiation axis specification protein localization localization cellular macromolecule localization cellular localization pole plasm protein localization macromolecule localization zygotic determination of anterior/posterior axis, embryo posterior abdomen determination response to light stimulus behavior response to stimulus visual behavior response to radiation response to abiotic stimulus system process learning learning or memory nervous system process visual learning cognition associative learning RNA localization pole plasm mRNA localization pole plasm RNA localization intracellular mRNA localization involved in anterior/posterior axis specification intracellular mRNA localization intracellular mRNA localization involved in pattern specification process long-term memory memory organelle organization actin cytoskeleton organization cortical actin cytoskeleton organization cortical cytoskeleton organization actin filament-based process cytoskeleton organization P granule organization non-membrane-bounded organelle assembly P granule assembly organelle assembly cellularization pole cell formation anatomical structure morphogenesis pole cell development anatomical structure formation involved in morphogenesis microtubule cytoskeleton organization establishment or maintenance of cell polarity establishment or maintenance of microtubule cytoskeleton polarity establishment or maintenance of cytoskeleton polarity oocyte microtubule cytoskeleton polarization microtubule-based process oocyte microtubule cytoskeleton organization organonitrogen compound biosynthetic process protein metabolic process organonitrogen compound metabolic process regulation of oskar mRNA translation regulation of protein metabolic process translation regulation of translation protein localization to organelle protein localization to nucleus thermosensory behavior response to temperature stimulus	intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle pole plasm intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle cell periphery intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle pole plasm intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle cell periphery cell cortex membrane-bounded organelle nucleus germ cell nucleus intracellular membrane-bounded organelle posterior cell cortex cell cortex region cytoplasmic region endosome intracellular vesicle endomembrane system cytoplasmic vesicle vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], D	IPR044763	Ded1/Dbp1, DEAD-box helicase domain	Domain
A [auth B], D	IPR001650	Helicase, C-terminal domain-like	Domain
A [auth B], D	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
A [auth B], D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A [auth B], D	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain
A [auth B], D	IPR011545	DEAD/DEAH box helicase domain	Domain
A [auth B], D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth A], C	IPR033447	OSK domain	Domain
B [auth A], C	IPR036514	SGNH hydrolase superfamily	Homologous Superfamily
B [auth A], C	IPR025605	OST-HTH/LOTUS domain	Domain
B [auth A], C	IPR041966	LOTUS-like domain	Homologous Superfamily

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 R01GM133198.