3RLS | pdb_00003rls

Crystal structure of yeast AF-9 homolog protein Yaf9

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3rlsb1	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	YEATS domain	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3rlsb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d3rlsa1	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	YEATS domain	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d3rlsa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	YEATS domain-like	8051393	4007347	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	YEATS domain-like	8053742	3002221	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	YEATS domain-like	8053742	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)
B	CagX	e3rlsB1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F: CagX	ECOD (develop294)
A	YEATS	e3rlsA1	A: alpha bundles	X: ETN0001 domain-like	H: ETN0001 domain-like	T: NAC/WRKY/GCM/WOPR domain	F: YEATS	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.1970	Mainly Beta	Sandwich	Immunoglobulin-like	YEATS domain	CATH (4.3.0)
A	2.60.40.1970	Mainly Beta	Sandwich	Immunoglobulin-like	YEATS domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	Protein AF-9 homolog	protein binding binding histone binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process subtelomeric heterochromatin formation negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair transcription by RNA polymerase II regulation of transcription by RNA polymerase II	protein-containing complex intracellular anatomical structure 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 intracellular organelle cellular anatomical structure protein-containing complex intracellular anatomical structure 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 intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex membrane-bounded organelle ATPase complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular organelle lumen histone deacetylase complex nucleoplasm SWI/SNF superfamily-type complex INO80-type complex intracellular membrane-bounded organelle Swr1 complex organelle lumen nuclear lumen cytoplasm chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.