9I8V | pdb_00009i8v

Cryo-EM structure of the Danio rerio tRNA ligase complex

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth F]	PF15323	Developmental protein (Ashwin)	Developmental protein	-	Family
D [auth E]	PF10036	RNA transcription, translation and transport factor protein (RLL)	RNA transcription, translation and transport factor protein	-	Family
C [auth D]	PF10239	Protein of unknown function (DUF2465) (DUF2465)	Protein of unknown function (DUF2465)	-	Family
B [auth C]	PF01139	tRNA-splicing ligase RtcB (RtcB)	tRNA-splicing ligase RtcB	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth F]	Ashwin	-	developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis embryonic morphogenesis anatomical structure development embryo development	tRNA-splicing ligase complex protein-containing complex catalytic complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
D [auth E]	RNA transcription, translation and transport factor protein	basal transcription machinery binding RNA polymerase binding protein binding binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding RNA binding nucleic acid binding	regulation of cellular process regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation negative regulation of biological process negative regulation of phosphate metabolic process negative regulation of catalytic activity regulation of transferase activity regulation of primary metabolic process negative regulation of kinase activity phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process protein metabolic process regulation of cellular process regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation negative regulation of biological process negative regulation of phosphate metabolic process negative regulation of catalytic activity regulation of transferase activity regulation of primary metabolic process negative regulation of kinase activity phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process protein metabolic process phosphorus metabolic process protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process biological regulation negative regulation of molecular function primary metabolic process negative regulation of protein kinase activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function regulation of kinase activity negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process cellular process metabolic process macromolecule metabolic process negative regulation of phosphorylation regulation of metabolic process RNA splicing RNA metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation nucleic acid biosynthetic process biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation tRNA processing RNA processing positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol perinuclear region of cytoplasm mitotic spindle intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol perinuclear region of cytoplasm mitotic spindle spindle tRNA-splicing ligase complex protein-containing complex catalytic complex intracellular protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C [auth D]	Family with sequence similarity 98, member B	-	-	tRNA-splicing ligase complex protein-containing complex catalytic complex intracellular protein-containing complex
B [auth C]	RNA-splicing ligase RtcB homolog	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ligase activity, forming phosphoric ester bonds RNA ligase (GTP) activity catalytic activity, acting on RNA RNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity ligase activity cation binding metal ion binding	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation nucleic acid biosynthetic process biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation tRNA processing RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation nucleic acid biosynthetic process biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation tRNA processing metabolic process cellular process RNA processing macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm tRNA-splicing ligase complex protein-containing complex catalytic complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
A [auth B]	ATP-dependent RNA helicase	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity RNA binding	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process macromolecule metabolic process RNA processing mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule cytosol nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth F]	IPR024887	Ashwin	Family
D [auth E]	IPR019265	RNA transcription, translation and transport factor protein	Family
C [auth D]	IPR018797	FAM98	Family
B [auth C]	IPR036025	tRNA-splicing ligase RtcB-like superfamily	Homologous Superfamily
B [auth C]	IPR027513	RNA-splicing ligase RtcB homologue, eukaryotic	Family
B [auth C]	IPR001233	RNA-splicing ligase, RtcB	Family
A [auth B]	IPR001870	B30.2/SPRY domain	Domain
A [auth B]	IPR001650	Helicase, C-terminal domain-like	Domain
A [auth B]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A [auth B]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A [auth B]	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
A [auth B]	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain
A [auth B]	IPR011545	DEAD/DEAH-box helicase domain	Domain
A [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth B]	IPR003877	SPRY 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.