1IG4

Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d1ig4a_	Alpha and beta proteins (a+b)	DNA-binding domain	DNA-binding domain	Methyl-CpG-binding domain, MBD	Methylation-dependent transcriptional repressor MBD1/PCM1	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)
C [auth A]	SCOP2 Family	Methyl-CpG-binding domain MBD	8021561	4000938	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	DNA-binding domain	8033941	3000183	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth A]	MBD	e1ig4A1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	3.30.890.10	Alpha Beta	2-Layer Sandwich	Methyl-cpg-binding Protein 2	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth 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 [auth B], B [auth C]	5'-D(GPTPAPTPCP(5CM)PGPGPAPTPAPC)-3'	-	-	-
C [auth A]	Methyl-CpG Binding Protein	DNA binding double-stranded DNA binding binding organic cyclic compound binding double-stranded methylated DNA binding nucleic acid binding protein-containing complex binding chromatin binding sequence-specific DNA binding unmethylated CpG binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding DNA binding double-stranded DNA binding binding organic cyclic compound binding double-stranded methylated DNA binding nucleic acid binding protein-containing complex binding chromatin binding sequence-specific DNA binding unmethylated CpG binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	regulation of cellular process negative regulation of biological process negative regulation of nitrogen compound metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process DNA-templated transcription regulation of RNA metabolic process heterocycle metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of cellular process negative regulation of biological process negative regulation of nitrogen compound metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process DNA-templated transcription regulation of RNA metabolic process heterocycle metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process aromatic compound biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process nitrogen compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process cellular aromatic compound metabolic process response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process cellular developmental process regulation of developmental process astrocyte differentiation cell development regulation of cell differentiation regulation of neurogenesis regulation of astrocyte differentiation regulation of gliogenesis regulation of cell development regulation of nervous system development multicellular organism development neurogenesis negative regulation of neurogenesis gliogenesis cell differentiation anatomical structure development regulation of multicellular organismal process negative regulation of nervous system development negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development negative regulation of developmental process regulation of glial cell differentiation nervous system development negative regulation of astrocyte differentiation negative regulation of gliogenesis negative regulation of cell development negative regulation of glial cell differentiation central nervous system development glial cell differentiation negative regulation of multicellular organismal process heart development animal organ development circulatory system development transcription by RNA polymerase II generation of neurons neuron differentiation response to extracellular stimulus response to nutrient levels response to external stimulus negative regulation of gene expression response to organic substance response to organonitrogen compound response to oxygen-containing compound response to nitrogen compound response to organic cyclic compound response to cocaine response to alkaloid response to lipid response to estradiol	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix nuclear speck membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix nuclear speck nuclear body nucleoplasm protein-containing complex protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR002857	Zinc finger, CXXC-type	Domain
C [auth A]	IPR016177	DNA-binding domain superfamily	Homologous Superfamily
C [auth A]	IPR001739	Methyl-CpG DNA binding	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A]	Pharos: Q9UIS9	prostate cancer B-cell chronic lymphocytic leukemia osteosarcoma Prostatic Neoplasms lung cancer ovarian cancer spina bifida malignant ependymoma subependymal giant cell astrocytoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.