7YZ8 | pdb_00007yz8

Triclinic crystal structure of YTHDF1 YTH domain (544AVV546 mutant)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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)
L	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PUA domain-like	8090676	3001015	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PUA domain-like	8090676	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)
L	YTH	e7yz8L1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
K	YTH	e7yz8K1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
J	YTH	e7yz8J1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
I	YTH	e7yz8I1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
H	YTH	e7yz8H1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
G	YTH	e7yz8G1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
F	YTH	e7yz8F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
E	YTH	e7yz8E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
D	YTH	e7yz8D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
C	YTH	e7yz8C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
B	YTH	e7yz8B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)
A	YTH	e7yz8A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: YTH	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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, E A, B, C, D, E, F, G, H, I, J, K, L	YTH domain-containing family protein 1	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 ribonucleoprotein complex binding protein-containing complex binding ribosome binding	immune system process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process immune system process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process antigen processing and presentation regulation of antigen processing and presentation regulation of immune system process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process 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 mRNA catabolic process negative regulation of metabolic process regulation of catabolic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of mRNA stability negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of RNA stability nucleic acid catabolic process regulation of mRNA metabolic process behavior multicellular organismal process system process learning learning or memory nervous system process cognition positive regulation of cell communication modulation of chemical synaptic transmission signaling cell communication long-term synaptic potentiation synaptic signaling regulation of synaptic plasticity trans-synaptic signaling regulation of signaling cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication positive regulation of signaling axonogenesis response to stimulus cell projection organization neuron projection development multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis taxis regulation of axon guidance cell differentiation anatomical structure development system development developmental process chemotaxis regulation of cell projection organization response to external stimulus nervous system development generation of neurons regulation of response to stimulus response to chemical regulation of locomotion regulation of neuron projection development regulation of cellular component organization cellular developmental process regulation of response to external stimulus plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis cellular component organization neurogenesis cellular component organization or biogenesis locomotion plasma membrane bounded cell projection organization axon guidance axon development regulation of chemotaxis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron projection guidance neuron development regulation of plasma membrane bounded cell projection organization cellular component biogenesis organelle organization cellular component assembly stress granule assembly organelle assembly membraneless organelle assembly memory 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 translational initiation regulation of translational initiation positive regulation of translational initiation	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 P-body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR007275	YTH domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR045168	YTH domain containing protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	Pharos: Q9BYJ9	astrocytic tumor ovarian cancer plasma cell myeloma glioblastoma pancreatic intraductal papillary-mucinous carcinoma psoriasis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm

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.