5ZUU

Crystal structure of AtCPSF30 YTH domain in complex with 10mer m6A-modified RNA

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth C]	PF04146	e5zuuC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PF04146	ECOD (1.6)
B [auth A]	PF04146	e5zuuA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PF04146	ECOD (1.6)
C [auth B]	PF04146	e5zuuB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PF04146	ECOD (1.6)
D	PF04146	e5zuuD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PF04146	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth C]	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (utative)
B [auth A]	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (utative)
C [auth B]	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (utative)
D	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth A], C [auth B], D	PF04146	YT521-B-like domain (YTH)	YT521-B-like domain	A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells [3]. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppr ...	A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells [3]. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein Swiss:Q9QY02 YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner [1]. The YTH domain has been identified as part of the PUA superfamily [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth A], C [auth B], D	30-kDa cleavage and polyadenylation specificity factor 30	DNA binding binding organic cyclic compound binding nucleic acid binding RNA binding mRNA binding protein binding calmodulin binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding RNA binding mRNA binding protein binding calmodulin binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity cation binding ion binding metal ion binding small molecule binding	cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process nucleic acid catabolic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process cellular response to stimulus biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response immune response defense response to symbiont response to external stimulus cell death response to biotic stimulus symbiont-induced defense-related programmed cell death cellular response to stress defense response to other organism response to stress immune system process plant-type hypersensitive response innate immune response response to external biotic stimulus programmed cell death regulation of biological process positive regulation of programmed cell death regulation of cellular process biological regulation positive regulation of biological process regulation of programmed cell death positive regulation of cellular process response to oxidative stress response to organic substance signaling regulation of signal transduction response to salicylic acid cell communication signal transduction cellular response to organic substance salicylic acid mediated signaling pathway response to organic cyclic compound cellular response to salicylic acid stimulus regulation of signaling regulation of salicylic acid mediated signaling pathway cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus regulation of response to stimulus response to chemical regulation of cell communication regulation of plant-type hypersensitive response regulation of defense response regulation of response to biotic stimulus positive regulation of response to biotic stimulus regulation of response to external stimulus regulation of cellular response to stress positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress regulation of immune system process positive regulation of immune system process positive regulation of innate immune response regulation of innate immune response positive regulation of defense response regulation of immune response positive regulation of plant-type hypersensitive response	intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle mRNA cleavage and polyadenylation specificity factor complex mRNA cleavage factor complex
E, F, G, H [auth I]	RNA (5'-R((6MZ)PCPUPAP*G)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth A], C [auth B], D	IPR007275	YTH domain	Domain
A [auth C], B [auth A], C [auth B], D	IPR000571	Zinc finger, CCCH-type	Domain
A [auth C], B [auth A], C [auth B], D	IPR045168	YTH domain containing protein	Family
A [auth C], B [auth A], C [auth B], D	IPR036855	Zinc finger, CCCH-type superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.