4WQN

Crystal structure of N6-methyladenosine RNA reader YTHDF2

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4wqna_	All beta proteins	PUA domain-like	PUA domain-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4wqnb_	All beta proteins	PUA domain-like	PUA domain-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PUA domain-like	8090678	3001015	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PUA domain-like	8090678	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	e4wqnA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
B	YTH	e4wqnB1	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	YTH domain-containing family protein 2	protein-RNA adaptor activity protein-macromolecule adaptor activity N6-methyladenosine-containing RNA reader activity molecular adaptor activity RNA binding binding nucleic acid binding mRNA binding C5-methylcytidine-containing RNA reader activity	developmental process stem cell proliferation cell population proliferation cellular developmental process hemopoiesis cell differentiation anatomical structure development hematopoietic stem cell proliferation cell development cellular process regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion developmental process stem cell proliferation cell population proliferation cellular developmental process hemopoiesis cell differentiation anatomical structure development hematopoietic stem cell proliferation cell development cellular process regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation regulation of developmental process regulation of cell differentiation regulation of hematopoietic stem cell differentiation stem cell differentiation regulation of stem cell differentiation hematopoietic stem cell differentiation regulation of hematopoietic progenitor cell differentiation hematopoietic progenitor cell differentiation multicellular organismal process regulation of multicellular organismal development regulation of neurogenesis nervous system development regulation of cell development regulation of nervous system development multicellular organism development neurogenesis regulation of multicellular organismal process system development 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 negative regulation of metabolic process 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 regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of mRNA metabolic process regulation of metabolic process sexual reproduction reproductive process multicellular organismal reproductive process gamete generation humoral immune response response to stimulus immune response immune system process negative regulation of stem cell differentiation negative regulation of developmental process negative regulation of cell differentiation cellular response to stimulus regulation of type I interferon-mediated signaling pathway response to cytokine regulation of signal transduction response to biotic stimulus cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus regulation of immune system process signal transduction response to other organism regulation of innate immune response negative regulation of immune response response to external stimulus regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus response to chemical defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response response to type I interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of signaling signaling negative regulation of cell communication cytokine-mediated signaling pathway response to stress regulation of response to stress innate immune response response to external biotic stimulus regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus defense response regulation of cytokine-mediated signaling pathway defense response to symbiont negative regulation of signal transduction response to peptide negative regulation of immune system process negative regulation of cytokine-mediated signaling pathway type I interferon-mediated signaling pathway regulation of cell communication negative regulation of type I interferon-mediated signaling pathway negative regulation of innate immune response ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process nucleobase-containing compound biosynthetic process regulation of rRNA processing positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of cap-independent translational initiation positive regulation of cap-independent translational initiation positive regulation of biosynthetic process translational initiation positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process cap-independent translational initiation regulation of translational initiation regulation of protein metabolic process translation positive regulation of gene expression regulation of translation positive regulation of cytoplasmic translational initiation regulation of cytoplasmic translational initiation cytoplasmic translation cytoplasmic translational initiation positive regulation of translational initiation regulation of cytoplasmic translation cell morphogenesis negative regulation of cell adhesion endothelial to hematopoietic transition anatomical structure morphogenesis cell-cell adhesion negative regulation of cell-cell adhesion regulation of cell-cell adhesion delamination embryonic morphogenesis embryo development Notch signaling pathway negative regulation of Notch signaling pathway regulation of Notch signaling pathway oogenesis cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction female gamete generation oocyte development anatomical structure maturation germ cell development oocyte maturation oocyte differentiation cell maturation spermatogenesis spermatogonial cell division male gamete generation cell division cellular component organization organelle organization cellular component assembly stress granule assembly organelle assembly membraneless organelle assembly meiotic cell cycle process involved in oocyte maturation regulation of reproductive process meiotic cell cycle process cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process meiotic cell cycle regulation of meiotic cell cycle process involved in oocyte maturation positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process mRNA destabilization RNA destabilization positive regulation of catabolic process positive regulation of mRNA catabolic process	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 centrosome microtubule organizing center cytoskeleton 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 centrosome microtubule organizing center cytoskeleton centriolar satellite microtubule cytoskeleton cytosol P-body membrane-bounded organelle nucleus intracellular membrane-bounded organelle

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9Y5A9	hepatocellular carcinoma Liver carcinoma

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.