4U8T | pdb_00004u8t

Crystal structure of YTH domain of Zygosaccharomyces rouxii MRB1 protein in complex with N6-Methyladenosine RNA

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)
A	d4u8ta1	All beta proteins	PUA domain-like	PUA domain-like	YTH domain	MRB1	(Zygosaccharomyces rouxii CBS 732 ) [TaxId: 559307 ],	SCOPe (2.08)
A	d4u8ta2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Zygosaccharomyces rouxii CBS 732 ) [TaxId: 559307 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	PUA domain-like	8090675	3001015	SCOP2B (2022-06-29)
E	SCOP2 Family	YTH domain-like	8045438	4004472	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	PUA domain-like	8090675	3001015	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	PUA domain-like	8090675	3001015	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PUA domain-like	8090675	3001015	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PUA domain-like	8090675	3001015	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PUA domain-like	8090675	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)
F	YTH	e4u8tF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
E	YTH	e4u8tE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
D	YTH	e4u8tD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
C	YTH	e4u8tC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
B	YTH	e4u8tB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
A	YTH	e4u8tA1	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)
F	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (4.3.0)
E	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (4.3.0)
D	3.10.590.10	Alpha Beta	Roll	ph1033 like fold	ph1033 like domains	CATH (4.3.0)
C	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)
A	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, C, D, E A, B, C, D, E, F	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
G [auth O], H [auth P], I [auth Q], J [auth R], K [auth S], G [auth O], H [auth P], I [auth Q], J [auth R], K [auth S], L [auth T]	RNA (5'-R(APGPGP(6MZ)PCPAP*U)-3')	-	-	-
A, B, C, D, E A, B, C, D, E, F	ZYRO0G01672p	RNA binding 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 cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process positive regulation of mRNA metabolic process primary metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process catabolic process positive regulation of biological process RNA metabolic process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability cellular process regulation of mRNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR007275	YTH domain	Domain
A, B, C, D, E A, B, C, D, E, F	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.