6CC8 | pdb_00006cc8

Crystal structure MBD3 MBD domain in complex with methylated CpG DNA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	DNA-binding domain	8081859	3000183	SCOP2B (2022-06-29)
A	SCOP2 Family	Methyl-CpG-binding domain, MBD	8081858	4000938	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA-binding domain	8081859	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)
B	MBD	e6cc8B1	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)
A	MBD	e6cc8A1	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)
B	3.30.890.10	Alpha Beta	2-Layer Sandwich	Methyl-cpg-binding Protein 2	Chain A	CATH (4.3.0)
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
A, B	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
C, D, E, F	methylated CpG DNA	-	-	-
A, B	Methyl-CpG-binding domain protein 3	DNA binding binding nucleic acid binding sequence-specific DNA binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding	regulation of cellular process negative regulation of biological 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 negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological 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 negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process regulation of developmental process cellular developmental process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation regulation of cell fate commitment cell fate specification regulation of cell fate specification cell fate commitment heart development multicellular organismal process cardiac muscle tissue development animal organ development tissue development striated muscle tissue development circulatory system development multicellular organism development ventricular cardiac muscle tissue development anatomical structure development muscle tissue development system development embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development embryonic organ development 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 constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic 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 RNA metabolic process positive regulation of RNA biosynthetic process response to nutrient levels response to stimulus transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II response to lipid response to chemical response to estradiol response to oxygen-containing compound	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex ATPase complex nuclear protein-containing complex transcription regulator complex histone deacetylase complex NuRD complex SWI/SNF superfamily-type complex catalytic complex CHD-type complex heterochromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR025884	Methyl-CpG binding protein 2/3, C-terminal domain	Domain
A, B	IPR016177	DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR001739	Methyl-CpG DNA binding	Domain
A, B	IPR032343	Methyl-CpG-binding domain protein 2/3, p55-binding region	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O95983	autism osteosarcoma Autistic Disorder ovarian cancer Hodgkins lymphoma psoriasis

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.