6SZX

Crystal structure of YTHDC1 with fragment 11 (DHU_DC1_128)

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	d6szxa1	All beta proteins	PUA domain-like	PUA domain-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6szxa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6szxb1	All beta proteins	PUA domain-like	PUA domain-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6szxb2	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)
A	SCOP2B Superfamily	PUA domain-like	8090679	3001015	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PUA domain-like	8090679	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	e6szxA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
B	YTH	e6szxB1	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 (utative)
B	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	YTHDC1	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding protein-RNA adaptor activity protein-macromolecule adaptor activity N6-methyladenosine-containing RNA reader activity molecular adaptor activity	developmental process sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation developmental process involved in reproduction gamete generation cell differentiation anatomical structure development germ cell development developmental process sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation developmental process involved in reproduction gamete generation cell differentiation anatomical structure development germ cell development cellular process primary follicle stage mammalian oogenesis stage regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process RNA processing regulation of biosynthetic process regulation of mRNA processing regulation of biological process RNA splicing cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome metabolic process regulation of macromolecule biosynthetic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process regulation of mRNA metabolic process regulation of metabolic process spermatogenesis male gamete generation ribonucleoprotein complex biogenesis protein-RNA complex assembly cellular component organization cellular component biogenesis spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis mRNA splice site recognition protein-containing complex organization negative regulation of biological process negative regulation of cellular metabolic process chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process heterochromatin formation sex-chromosome dosage compensation epigenetic regulation of gene expression negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process dosage compensation by inactivation of X chromosome negative regulation of gene expression, epigenetic cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport intracellular transport establishment of localization RNA export from nucleus establishment of RNA localization macromolecule localization mRNA 3'-end processing mRNA alternative polyadenylation RNA 3'-end processing alternative mRNA splicing, via spliceosome regulation of alternative mRNA splicing, via spliceosome post-transcriptional regulation of gene expression multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cell periphery plasma membrane membrane

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: Q96MU7	amyotrophic lateral sclerosis juvenile dermatomyositis ovarian cancer tuberculosis breast cancer myopathy plasma cell myeloma dermatomyositis osteosarcoma spina bifida

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.