5VNA | pdb_00005vna

Crystal structure of human YEATS 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)
D	d5vnad_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5vnac_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5vnab_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5vnaa_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	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)
D	SCOP2B Superfamily	YEATS domain-like	8053748	3002221	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YEATS domain-like	8053748	3002221	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YEATS domain-like	8053748	3002221	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	YEATS domain-like	8053748	3002221	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)
D	YEATS	e5vnaD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: C2 domain (From Topology)	T: C2 domain	F: YEATS	ECOD (1.6)
C	YEATS	e5vnaC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: C2 domain (From Topology)	T: C2 domain	F: YEATS	ECOD (1.6)
B	YEATS	e5vnaB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: C2 domain (From Topology)	T: C2 domain	F: YEATS	ECOD (1.6)
A	YEATS	e5vnaA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: C2 domain (From Topology)	T: C2 domain	F: YEATS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.40.1970	Mainly Beta	Sandwich	Immunoglobulin-like	YEATS domain	CATH (utative)
C	2.60.40.1970	Mainly Beta	Sandwich	Immunoglobulin-like	YEATS domain	CATH (utative)
B	2.60.40.1970	Mainly Beta	Sandwich	Immunoglobulin-like	YEATS domain	CATH (utative)
A	2.60.40.1970	Mainly Beta	Sandwich	Immunoglobulin-like	YEATS domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03366	YEATS family (YEATS)	YEATS family	We have named this family the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit'. This family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	YEATS domain-containing protein 4	protein binding binding histone binding structural constituent of cytoskeleton structural molecule activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity histone H3K27ac reader activity molecular adaptor activity histone H3K18ac reader activity	cellular process cell cycle mitotic cell cycle cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus cellular process cell cycle mitotic cell cycle cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair cellular response to stress response to stress regulation of response to stress recombinational repair positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination positive regulation of cellular process DNA repair positive regulation of DNA recombination double-strand break repair regulation of biological process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of double-strand break repair regulation of DNA repair regulation of double-strand break repair via homologous recombination positive regulation of DNA metabolic process DNA damage response regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death regulation of cell cycle cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix protein-containing complex catalytic complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix protein-containing complex catalytic complex NuA4 histone acetyltransferase complex intracellular membraneless organelle chromatin chromosome transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex membraneless organelle protein acetyltransferase complex intracellular protein-containing complex nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane protein-DNA complex nucleosome nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR038704	YEATS superfamily	Homologous Superfamily
A, B, C, D	IPR005033	YEATS	Family
A, B, C, D	IPR055129	YEATS domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O95619	liposarcoma pleomorphic liposarcoma attention deficit hyperactivity disorder, inattentive type medulloblastoma Dedifferentiated liposarcoma lung cancer glioblastoma malignant mesothelioma 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.