5AGQ

Solution structure of the TAM domain of human TIP5 BAZ2A involved in epigenetic regulation of rRNA genes

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	MBD	e5agqA1	A: a+b two layers	X: DNA-binding domain	H: Methyl-CpG-binding domain, MBD (From Topology)	T: Methyl-CpG-binding domain, MBD	F: MBD	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01429	Methyl-CpG binding domain (MBD)	Methyl-CpG binding domain	The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs [1]. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-s ...	The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs [1]. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair [1]. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2A	protein binding binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein binding RNA binding nucleic acid binding DNA binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding cation binding protein binding binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein binding RNA binding nucleic acid binding DNA binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding cation binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription transcription preinitiation complex assembly RNA polymerase I preinitiation complex assembly cellular component biogenesis protein-DNA complex organization transcription initiation at RNA polymerase I promoter cellular component assembly transcription by RNA polymerase I protein-containing complex assembly protein-containing complex organization protein-DNA complex assembly DNA-templated transcription initiation nucleolar chromatin organization rDNA heterochromatin formation nucleus organization organelle organization nucleolus organization facultative heterochromatin formation negative regulation of RNA biosynthetic process negative regulation of transcription by RNA polymerase I negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of transcription by RNA polymerase I negative regulation of RNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nuclear speck nuclear body nucleoplasm cytoplasm cytosol ATPase complex protein-containing complex catalytic complex nuclear protein-containing complex chromatin chromosome ISWI-type complex SWI/SNF superfamily-type complex NoRC complex chromatin silencing complex rDNA heterochromatin heterochromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR037374	BAZ2A/BAZ2B, bromodomain	Domain
A	IPR018359	Bromodomain, conserved site	Conserved Site
A	IPR028941	WHIM2 domain	Domain
A	IPR001487	Bromodomain	Domain
A	IPR018501	DDT domain	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR028940	Bromodomain adjacent to zinc finger domain protein 2A, PHD zinc finger	Domain
A	IPR016177	DNA-binding domain superfamily	Homologous Superfamily
A	IPR028942	WHIM1 domain	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR001739	Methyl-CpG DNA binding	Domain
A	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A	IPR017956	AT hook, DNA-binding motif	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9UIF9	prostate cancer acute myeloid leukemia malignant mesothelioma Prostatic Neoplasms atrial fibrillation osteosarcoma psoriasis lung cancer

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.