9H35

Crystal structure of the YTHDC2 YTH domain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PUA domain-like	8090682	3001015	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PUA domain-like	8090682	3001015	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PUA domain-like	8090682	3001015	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PUA domain-like	8090682	3001015	SCOP2B (2022-06-29)

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	3'-5' RNA helicase YTHDC2	ATP-dependent activity, acting on DNA catalytic activity, acting on DNA DNA translocase activity catalytic activity, acting on a nucleic acid chromatin extrusion motor activity catalytic activity ATP-dependent activity helicase activity ATP-dependent H3-H4 histone complex chaperone activity catalytic activity, acting on a protein histone chaperone activity ATP-dependent chromatin remodeler activity H3-H4 histone complex chaperone activity protein carrier chaperone ATP-dependent activity, acting on DNA catalytic activity, acting on DNA DNA translocase activity catalytic activity, acting on a nucleic acid chromatin extrusion motor activity catalytic activity ATP-dependent activity helicase activity ATP-dependent H3-H4 histone complex chaperone activity catalytic activity, acting on a protein histone chaperone activity ATP-dependent chromatin remodeler activity H3-H4 histone complex chaperone activity protein carrier chaperone ATP-dependent histone chaperone activity molecular carrier activity protein-RNA adaptor activity protein-macromolecule adaptor activity N6-methyladenosine-containing RNA reader activity molecular adaptor activity cohesin loader activity DNA clamp loader activity ATP-dependent H2AZ histone chaperone activity RNA polymerase binding protein binding binding enzyme binding catalytic activity, acting on RNA 3'-5' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA RNA binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	modulation by host of viral process biological process involved in interspecies interaction between organisms viral genome replication viral process positive regulation by host of viral process viral life cycle positive regulation by host of viral genome replication modulation of process of another organism host-mediated perturbation of symbiont process modulation by host of viral genome replication developmental process sexual reproduction cellular developmental process reproductive process modulation by host of viral process biological process involved in interspecies interaction between organisms viral genome replication viral process positive regulation by host of viral process viral life cycle positive regulation by host of viral genome replication modulation of process of another organism host-mediated perturbation of symbiont process modulation by host of viral genome replication developmental process sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation oocyte development cell differentiation anatomical structure development germ cell development cellular process oocyte differentiation response to peptide response to stimulus response to chemical response to cytokine response to interleukin-1 spermatid development spermatid differentiation spermatogenesis male gamete generation cell cycle switching regulation of cellular process regulation of reproductive process negative regulation of biological process positive regulation of biological process negative regulation of cell cycle negative regulation of mitotic cell cycle mitotic cell cycle regulation of mitotic cell cycle germline cell cycle switching, mitotic to meiotic cell cycle negative regulation of cellular process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process positive regulation of reproductive process regulation of biological process regulation of meiotic cell cycle meiotic cell cycle biological regulation positive regulation of meiotic cell cycle positive regulation of cell cycle cell cycle switching, mitotic to meiotic cell cycle response to tumor necrosis factor	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle supramolecular complex ribonucleoprotein granule perinuclear region of cytoplasm cytoplasm membrane-bounded organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007275	YTH domain	Domain
A, B, C, D	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR001374	R3H domain	Domain
A, B, C, D	IPR034083	DExH-box ATP-dependent RNA helicase, R3H domain	Domain
A, B, C, D	IPR048333	Helicase associated domain (HA2), winged-helix domain	Domain
A, B, C, D	IPR011545	DEAD/DEAH box helicase domain	Domain
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR002110	Ankyrin repeat	Repeat
A, B, C, D	IPR011709	DEAD-box helicase, OB fold	Domain
A, B, C, D	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C, D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C, D	IPR036867	R3H domain superfamily	Homologous Superfamily
A, B, C, D	IPR007502	Helicase-associated domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9H6S0	Alzheimer disease osteosarcoma progressive supranuclear palsy large cell medulloblastoma ovarian cancer psoriasis medulloblastoma Pick disease rheumatoid arthritis

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.