Annotations: 3HGQ

Structural and functional studies of the yeast class II Hda1 HDAC complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	YgbB	e3hgqD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v294.1)
C	YgbB	e3hgqC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v294.1)
B	YgbB	e3hgqB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v294.1)
A	EF-hand_1, EF-hand_6, EF-hand_7	e3hgqA1	A: a/b three-layered sandwiches	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Provenance Source (Version)
D	3.40.50.12360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
C	3.40.50.12360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
B	3.40.50.12360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
A	3.40.50.12360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	HDA1 complex subunit 3	DNA binding binding nucleic acid binding ATP-dependent activity, acting on DNA nucleosome array spacer activity ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA histone octamer slider activity catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity chromatin binding	regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression, epigenetic cell cycle chromosome segregation cell cycle process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex catalytic complex HDA1 complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex catalytic complex HDA1 complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR026216	HDA1 complex subunit 3	Family
A, B, C, D	IPR021006	HDA1 complex subunit 2/3	Family
A, B, C, D	IPR038609	HDA1 complex subunit 2/3 superfamily	Homologous Superfamily

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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.

3HGQ | pdb_00003hgq

Structural and functional studies of the yeast class II Hda1 HDAC complex

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage