5O8M | pdb_00005o8m

Crystal structure of the MmI1 YTH domain

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d5o8md_	All beta proteins	PUA domain-like	PUA domain-like	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
C	d5o8mc_	All beta proteins	PUA domain-like	PUA domain-like	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
B	d5o8mb_	All beta proteins	PUA domain-like	PUA domain-like	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
A	d5o8ma_	All beta proteins	PUA domain-like	PUA domain-like	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PUA domain-like	8090677	3001015	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PUA domain-like	8090677	3001015	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PUA domain-like	8090677	3001015	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PUA domain-like	8090677	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)
D	YTH	e5o8mD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
C	YTH	e5o8mC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
B	YTH	e5o8mB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
A	YTH	e5o8mA1	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)
D	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (utative)
C	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (utative)
B	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (utative)
A	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, B, C, 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, B, C, D	YTH domain-containing protein mmi1	pre-mRNA binding RNA binding binding nucleic acid binding lncRNA binding protein-RNA adaptor activity protein-macromolecule adaptor activity N6-methyladenosine-containing RNA reader activity molecular adaptor activity mRNA 3'-UTR binding mRNA binding protein-containing complex binding CCR4-NOT complex binding pre-mRNA intronic binding	regulation of cellular process negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of cellular process negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation siRNA-independent facultative heterochromatin formation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process facultative heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process nuclear RNA surveillance catabolic process RNA metabolic process nuclear polyadenylation-dependent CUT catabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process CUT catabolic process nucleic acid catabolic process RNA surveillance RNA catabolic process lncRNA catabolic process nuclear mRNA surveillance of mRNA 3'-end processing mRNA catabolic process nuclear-transcribed mRNA catabolic process nuclear mRNA surveillance mRNA metabolic process regulation of termination of RNA polymerase II transcription regulation of cellular component organization protein-containing complex disassembly DNA-templated transcription termination regulation of protein-containing complex disassembly regulation of primary metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of termination of RNA polymerase II transcription, poly(A)-coupled regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process cellular component disassembly termination of RNA polymerase II transcription, poly(A)-coupled protein-containing complex organization nucleobase-containing compound biosynthetic process regulation of termination of DNA-templated transcription termination of RNA polymerase II transcription regulatory ncRNA-mediated gene silencing regulation of heterochromatin formation regulation of chromatin organization regulation of siRNA-independent facultative heterochromatin formation RNA 3'-end processing RNA processing regulatory ncRNA 3'-end processing regulatory ncRNA processing nuclear lncRNA surveillance positive regulation of metabolic process post-transcriptional regulation of gene expression positive regulation of macromolecule metabolic process regulation of biological quality 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 mRNA destabilization regulation of mRNA catabolic process positive regulation of cellular process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process nuclear mRNA surveillance of spliceosomal pre-mRNA splicing nuclear mRNA surveillance of meiosis-specific transcripts	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle heterochromatin island chromatin chromosome heterochromatin membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle heterochromatin island chromatin chromosome heterochromatin membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nuclear exosome focus intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen cytoplasm protein-containing complex nuclear protein-containing complex Mei2 nuclear dot complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

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

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.