5YKI | pdb_00005yki

Crystal structure of the engineered nine-repeat PUF domain in complex with cognate 9nt-RNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ARM repeat-like	8043381	3000116	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00806	Pumilio-family RNA binding repeat (PUF)	Pumilio-family RNA binding repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	RNA (5'-R(UPGPUPUPGPUPAPUP*A)-3')	-	-	-
A	Pumilio homolog 1	mRNA 3'-UTR binding RNA binding binding nucleic acid binding mRNA binding regulatory RNA binding miRNA binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of mRNA catabolic process negative regulation of cellular process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of mRNA stability regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of RNA stability nucleic acid catabolic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of mRNA metabolic process regulation of metabolic process adult locomotory behavior behavior multicellular organismal process adult behavior locomotory behavior positive regulation of biological process regulation of miRNA-mediated gene silencing positive regulation of post-transcriptional gene silencing positive regulation of miRNA-mediated gene silencing regulation of gene silencing by regulatory ncRNA positive regulation of post-transcriptional gene silencing by RNA regulation of post-transcriptional gene silencing by regulatory ncRNA regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing regulation of post-transcriptional gene silencing post-transcriptional gene silencing regulation of protein metabolic process translation protein biosynthetic process regulation of translation protein metabolic process 3'-UTR-mediated mRNA destabilization positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process mRNA destabilization positive regulation of cellular process RNA destabilization positive regulation of catabolic process positive regulation of mRNA catabolic process cellular response to stimulus positive regulation of cell communication positive regulation of response to biotic stimulus positive regulation of signal transduction pattern recognition receptor signaling pathway response to stimulus regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus positive regulation of intracellular signal transduction regulation of RIG-I signaling pathway RIG-I signaling pathway regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response positive regulation of RIG-I signaling pathway 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 positive regulation of response to stimulus 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 regulation of signaling positive regulation of innate immune response defense response defense response to symbiont immune system process regulation of cell communication positive regulation of signaling regulation of chromosome segregation regulation of cell cycle process cell cycle regulation of cell cycle chromosome segregation cell cycle process stem cell differentiation cellular developmental process cell differentiation RNA biosynthetic process nucleic acid biosynthetic process RNA processing nucleobase-containing compound biosynthetic process regulatory ncRNA processing miRNA processing	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cytosol membrane-bounded organelle nucleus intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen axon cell projection neuron projection plasma membrane bounded cell projection P-body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR011989	Armadillo-like helical	Homologous Superfamily
A	IPR001313	Pumilio RNA-binding repeat	Repeat
A	IPR033712	Pumilio, RNA binding domain	Domain
A	IPR033133	Pumilio homology domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q14671	autosomal dominant cerebellar ataxia neurodegenerative disease plasma cell myeloma drug-induced liver injury osteosarcoma spinocerebellar ataxia 47 lung adenocarcinoma ovarian 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.