8AJR | pdb_00008ajr

The Solution Structure of the Triple Mutant Methyl-CpG-Binding Domain from MeCP2

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	SCOP2B Superfamily	DNA-binding domain	8034362	3000183	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)
A	F5_F8_type_C	e8ajrA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (v294.1)

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	Methyl-CpG-binding protein 2	binding nucleic acid binding chromatin binding promoter-specific chromatin binding DNA binding RNA binding mRNA binding histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity sequence-specific DNA binding nucleoside phosphate binding nucleotide binding binding nucleic acid binding chromatin binding promoter-specific chromatin binding DNA binding RNA binding mRNA binding histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity sequence-specific DNA binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding regulatory RNA binding siRNA binding double-stranded DNA binding double-stranded methylated DNA binding molecular condensate scaffold activity transcription corepressor activity transcription regulator activity transcription coregulator activity	multicellular organismal process system process nervous system process sensory perception neuromuscular process proprioception neuromuscular process controlling posture respiratory gaseous exchange by respiratory system biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to external stimulus response to external biotic stimulus response to biotic stimulus multicellular organismal process system process nervous system process sensory perception neuromuscular process proprioception neuromuscular process controlling posture respiratory gaseous exchange by respiratory system biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to external stimulus response to external biotic stimulus response to biotic stimulus glycerophospholipid metabolic process primary metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process phosphatidylcholine metabolic process glycerolipid metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process developmental process head development animal organ development brain development nervous system development multicellular organism development cerebellum development central nervous system development metencephalon development anatomical structure development hindbrain development system development regulation of biological process smooth muscle cell differentiation regulation of cellular process regulation of developmental process cellular developmental process negative regulation of developmental process biological regulation negative regulation of biological process regulation of smooth muscle cell differentiation negative regulation of muscle cell differentiation regulation of cell differentiation muscle cell differentiation muscle structure development negative regulation of smooth muscle cell differentiation regulation of muscle cell differentiation cell differentiation negative regulation of cellular process negative regulation of cell differentiation startle response negative regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration regulation of locomotion regulation of cell migration regulation of endothelial cell migration negative regulation of cell motility blood vessel endothelial cell migration cell migration cell motility locomotion negative regulation of cell migration response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process L-glutamine metabolic process proteinogenic amino acid metabolic process small molecule metabolic process amine metabolic process biogenic amine metabolic process regulation of systemic arterial blood pressure circulatory system process regulation of blood pressure regulation of biological quality nervous system process involved in regulation of systemic arterial blood pressure blood circulation 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 negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of 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 regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular response to stimulus cell surface receptor signaling pathway signaling cell communication Notch signaling pathway signal transduction cellular component organization cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization cellular component organization or biogenesis synapse assembly ventricular system development 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 monoamine transport nitrogen compound transport transport secretion export from cell organic hydroxy compound transport establishment of localization catecholamine secretion localization secretion by cell catecholamine transport polyol metabolic process inositol metabolic process alcohol metabolic process adult locomotory behavior behavior adult behavior locomotory behavior phosphatidylglycerol metabolic process cardiolipin metabolic process negative regulation of gene expression via chromosomal CpG island methylation chromatin organization chromatin remodeling epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic glucocorticoid metabolic process steroid metabolic process cell development developmental maturation generation of neurons neurogenesis neuron differentiation anatomical structure maturation neuron development neuron maturation cell maturation regulation of system process respiratory system process regulation of respiratory gaseous exchange regulation of multicellular organismal process regulation of respiratory system process regulation of respiratory gaseous exchange by nervous system process positive regulation of organelle organization regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of cellular component organization positive regulation of cellular component organization microtubule cytoskeleton organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly microtubule polymerization or depolymerization positive regulation of protein polymerization protein-containing complex assembly protein polymerization positive regulation of microtubule nucleation positive regulation of microtubule polymerization or depolymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of microtubule-based process microtubule polymerization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of microtubule nucleation regulation of organelle organization organelle organization microtubule nucleation regulation of microtubule polymerization regulation of protein polymerization positive regulation of microtubule polymerization regulation of supramolecular fiber organization microtubule-based process supramolecular fiber organization cytoskeleton organization regulation of microtubule cytoskeleton organization response to light stimulus learning learning or memory visual learning visual behavior cognition associative learning response to radiation neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of neuron apoptotic process long-term memory memory regulation of postsynaptic membrane potential chemical synaptic transmission, postsynaptic synaptic signaling trans-synaptic signaling cell-cell signaling chemical synaptic transmission anterograde trans-synaptic signaling excitatory postsynaptic potential regulation of membrane potential plasma membrane bounded cell projection organization cell projection organization neuron projection development dendrite development trans-synaptic signaling by BDNF heterochromatin formation heterochromatin organization biological process involved in intraspecies interaction between organisms social behavior behavioral defense response fear response behavioral fear response defense response multicellular organismal response to stress sensory perception of pain angiogenesis regulation of vasculature development tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process sexual reproduction reproductive process cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation epigenetic programming of gene expression multicellular organismal reproductive process genomic imprinting germ cell development positive regulation of nervous system development positive regulation of cell population proliferation regulation of neurogenesis regulation of gliogenesis positive regulation of glial cell proliferation positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process regulation of glial cell proliferation gliogenesis positive regulation of cell differentiation positive regulation of neurogenesis cell population proliferation positive regulation of cell development regulation of cell population proliferation positive regulation of multicellular organismal process glial cell proliferation positive regulation of cell communication modulation of chemical synaptic transmission long-term synaptic potentiation regulation of synaptic plasticity regulation of signaling positive regulation of synaptic transmission regulation of trans-synaptic signaling regulation of cell communication positive regulation of signaling post-embryonic development macromolecule localization intracellular protein localization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin postsynapse synapse cell junction cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin postsynapse synapse cell junction centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016177	DNA-binding domain superfamily	Homologous Superfamily
A	IPR017353	Methyl-CpG binding protein MeCP2	Family
A	IPR001739	Methyl-CpG DNA binding	Domain
A	IPR045138	Methyl-CpG binding protein MeCP2/MBD4	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P51608	Rett syndrome severe neonatal-onset encephalopathy with microcephaly syndromic X-linked intellectual disability Lubs type Angelman syndrome intellectual disability X-linked intellectual disability-psychosis-macroorchidism syndrome visual epilepsy pervasive developmental disorder pulmonary fibrosis atypical Rett syndrome autism, susceptibility to, X-linked 3 cocaine abuse MECP2 duplication syndrome epilepsy rheumatoid arthritis Rett syndrome severe neonatal-onset encephalopathy with microcephaly syndromic X-linked intellectual disability Lubs type Angelman syndrome intellectual disability X-linked intellectual disability-psychosis-macroorchidism syndrome visual epilepsy pervasive developmental disorder pulmonary fibrosis atypical Rett syndrome autism, susceptibility to, X-linked 3 cocaine abuse MECP2 duplication syndrome epilepsy rheumatoid arthritis autism cocaine dependence respiratory failure malignant mesothelioma anxiety disorder hepatocellular carcinoma subependymal giant cell astrocytoma learning disability osteosarcoma developmental disability microcephaly fragile X syndrome astrocytic tumor idiopathic interstitial pneumonia large cell medulloblastoma malignant glioma autism spectrum disorder Sjogren syndrome celiac disease systemic lupus erythematosus

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.