Annotations: 4QBQ

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF17980	e4qbqA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PF17980	ECOD (1.6)
A	PF21255	e4qbqA2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PF21255	ECOD (1.6)
B [auth C]	PF17980	e4qbqC1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PF17980	ECOD (1.6)
B [auth C]	PF21255	e4qbqC2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PF21255	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C]	PF21255	DNMT3, ADD PHD zinc finger (DNMT3_ADD_GATA1-like)	DNMT3, ADD PHD zinc finger	DNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes [1-4]. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger (Pfam:PF17980) and a PHD-like zinc fin ...	DNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes [1-4]. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger (Pfam:PF17980) and a PHD-like zinc finger, represented in this entry. In this domain, the conserved His residue observed in classical PHD zinc fingers is replaced by a cysteine.	Domain
A, B [auth C]	PF17980	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger (ADD_DNMT3)	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	This is a C4-type GATA1-like zinc finger of a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in animal DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome ...	This is a C4-type GATA1-like zinc finger of a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in animal DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome with chromatin containing methylated H3K4. This domain contains two parts, a GATA1-like and a PHD-like (Pfam:PF21255) zinc fingers. The DNA methyltransferase (DNMT) 3 family members DNMT3A and the DNMT3-like non-enzymatic regulatory factor DNMT3L, are involved in de-novo establishment of DNA methylation patterns in early mammalian development [1,2].	Domain
C [auth P]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C]	DNA (cytosine-5)-methyltransferase 3A	sequence-specific DNA binding DNA binding binding organic cyclic compound binding unmethylated CpG binding nucleic acid binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity transferase activity methyltransferase activity protein-cysteine methyltransferase activity catalytic activity sequence-specific DNA binding DNA binding binding organic cyclic compound binding unmethylated CpG binding nucleic acid binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity transferase activity methyltransferase activity protein-cysteine methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein-containing complex binding chromatin binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid	response to stimulus response to chemical response to xenobiotic stimulus regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process response to stimulus response to chemical response to xenobiotic stimulus regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process 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 protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process 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 gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation response to decreased oxygen levels cellular response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus methylation S-adenosylmethionine metabolic process sulfur compound metabolic process response to nutrient levels response to organic substance response to lipid response to nutrient response to vitamin A response to vitamin response to toxic substance response to ionizing radiation response to radiation cellular response to bisphenol A cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to organic substance response to organic cyclic compound response to bisphenol A cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid response to alcohol cellular response to alcohol cellular response to ethanol response to ethanol regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II primary metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of cellular response to hypoxia positive regulation of biological process regulation of cellular response to stress positive regulation of response to stimulus regulation of response to stress positive regulation of cellular response to hypoxia positive regulation of cellular process regulation of response to stimulus multicellular organismal process cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development system development DNA methylation-dependent heterochromatin formation heterochromatin formation facultative heterochromatin formation epigenetic programming of gene expression response to metal ion response to lead ion response to inorganic substance cell development cellular process involved in reproduction in multicellular organism genomic imprinting autosome genomic imprinting germ cell development hepatocyte apoptotic process apoptotic process cell death programmed cell death epithelial cell apoptotic process response to organonitrogen compound response to nitrogen compound response to cocaine response to alkaloid response to estradiol	intracellular organelle XY body intracellular anatomical structure sex chromosome organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle cytoplasm protein-containing complex protein-DNA complex chromatin heterochromatin intracellular organelle XY body intracellular anatomical structure sex chromosome organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle cytoplasm protein-containing complex protein-DNA complex chromatin heterochromatin membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen nuclear matrix chromosome, centromeric region chromosomal region catalytic complex nucleoplasm euchromatin
C [auth P]	Histone H3	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organic substance metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-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, B [auth C]	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
A, B [auth C]	IPR044108	DNA (cytosine-5)-methyltransferase 3A, ADD domain	Domain
A, B [auth C]	IPR000313	PWWP domain	Domain
A, B [auth C]	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A, B [auth C]	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
A, B [auth C]	IPR001525	C-5 cytosine methyltransferase	Family
A, B [auth C]	IPR025766	ADD domain	Domain
A, B [auth C]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
C [auth P]	IPR009072	Histone-fold	Homologous Superfamily
C [auth P]	IPR007125	Histone H2A/H2B/H3	Domain
C [auth P]	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth C]	Pharos: Q9Y6K1	tall stature-intellectual disability-facial dysmorphism syndrome Crohn disease acute monocytic leukemia juvenile myelomonocytic leukemia intellectual disability acute myeloid leukemia breast cancer chronic myelomonocytic leukemia primary cutaneous T-cell non-Hodgkin lymphoma acute promyelocytic leukemia breast carcinoma Clear-cell metastatic renal cell carcinoma mature T-cell and NK-cell non-Hodgkin lymphoma Sezary syndrome angioimmunoblastic T-cell lymphoma tall stature-intellectual disability-facial dysmorphism syndrome Crohn disease acute monocytic leukemia juvenile myelomonocytic leukemia intellectual disability acute myeloid leukemia breast cancer chronic myelomonocytic leukemia primary cutaneous T-cell non-Hodgkin lymphoma acute promyelocytic leukemia breast carcinoma Clear-cell metastatic renal cell carcinoma mature T-cell and NK-cell non-Hodgkin lymphoma Sezary syndrome angioimmunoblastic T-cell lymphoma microcephaly non-small cell lung carcinoma ductal breast carcinoma in situ pancreatic intraductal papillary-mucinous neoplasm genetic endocrine growth disease primary biliary cholangitis ileocolitis systemic mastocytosis lung cancer atypical teratoid rhabdoid tumor malignant ependymoma congenital anemia Crohn's colitis myelodysplastic syndrome oligodendroglioma glioblastoma hematologic disease large cell medulloblastoma autism spectrum disorder malignant glioma osteosarcoma plasma cell myeloma granulomatous slack skin disease hypertensive disorder primitive neuroectodermal tumor invasive ductal breast carcinoma lung benign neoplasm malignant mesothelioma cancer medulloblastoma
C [auth P]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma

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 R01GM133198.