4RCM

Crystal structure of the Pho92 YTH domain in complex with m6A

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	YTH domain-like	8045444	4004472	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PUA domain-like	8090681	3001015	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PUA domain-like	8090681	3001015	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	YTH	e4rcmA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
B	YTH	e4rcmB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (4.3.0)
B	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	Methylated RNA-binding protein 1	mRNA 3'-UTR binding RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding protein-RNA adaptor activity protein-macromolecule adaptor activity N6-methyladenosine-containing RNA reader activity molecular adaptor activity	regulation of biological process regulation of cellular process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process regulation of phosphorus metabolic process metabolic process cellular process phosphorus metabolic process regulation of metabolic process negative regulation of biological process negative regulation of cellular metabolic process regulation of biological process regulation of cellular process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process regulation of phosphorus metabolic process metabolic process cellular process phosphorus metabolic process regulation of metabolic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process cellular catabolic process nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process heterocycle metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process negative regulation of metabolic process cellular nitrogen compound metabolic process primary metabolic process aromatic compound catabolic process negative regulation of cellular biosynthetic process cellular nitrogen compound catabolic 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 heterocycle catabolic process nucleic acid catabolic process regulation of macromolecule biosynthetic process macromolecule 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 nitrogen compound metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of catabolic process regulation of macromolecule metabolic 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 regulation of cellular catabolic process regulation of mRNA metabolic process organic substance catabolic process cellular aromatic compound metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process positive regulation of biological process positive regulation of cellular metabolic process mRNA destabilization positive regulation of cellular process RNA destabilization positive regulation of catabolic process positive regulation of nitrogen compound metabolic process positive regulation of mRNA catabolic process positive regulation of cellular catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity
C [auth D], D [auth E]	RNA (5'-R(UPG)-D((6MZ)PCP*U)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007275	YTH domain	Domain
A, B	IPR045168	YTH domain containing protein	Family

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.