6K6U | pdb_00006k6u

Crystal structure of the human YTHDC2 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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6k6ub_	All beta proteins	PUA domain-like	PUA domain-like	YTH domain	YTHDC1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6k6ua1	All beta proteins	PUA domain-like	PUA domain-like	YTH domain	YTHDC1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6k6ua2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
B	SCOP2B Superfamily	PUA domain-like	8090682	3001015	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PUA domain-like	8090682	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)
B	YTH	e6k6uB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
A	YTH	e6k6uA1	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)
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	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	3'-5' RNA helicase YTHDC2	nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity protein-RNA adaptor activity protein-macromolecule adaptor activity N6-methyladenosine-containing RNA reader activity molecular adaptor activity RNA polymerase binding protein binding binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity protein-RNA adaptor activity protein-macromolecule adaptor activity N6-methyladenosine-containing RNA reader activity molecular adaptor 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	host-mediated activation of viral genome replication biological process involved in interspecies interaction between organisms host-mediated perturbation of viral genome replication host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process host-mediated activation of viral process developmental process sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process oogenesis cell development host-mediated activation of viral genome replication biological process involved in interspecies interaction between organisms host-mediated perturbation of viral genome replication host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process host-mediated activation of viral process 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	IPR007275	YTH domain	Domain
A, B	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR001374	R3H domain	Domain
A, B	IPR034083	DExH-box ATP-dependent RNA helicase, R3H domain	Domain
A, B	IPR048333	Helicase associated domain (HA2), winged-helix domain	Domain
A, B	IPR011545	DEAD/DEAH-box helicase domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR002110	Ankyrin repeat	Repeat
A, B	IPR011709	DEAD-box helicase, OB fold	Domain
A, B	IPR001650	Helicase, C-terminal domain-like	Domain
A, B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B	IPR036867	R3H domain superfamily	Homologous Superfamily
A, B	IPR007502	Helicase-associated domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	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.