Annotations: 8EIH

Cryo-EM structure of human DNMT3B homo-tetramer (form I)

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)
E	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8067898	3000404	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)
E	Cation_efflux	e8eihE1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cation_efflux	ECOD (v295.2)
D	Polyketide_cyc2	e8eihD1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v295.2)
C	Polyketide_cyc2	e8eihC1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v295.2)
B	Polyketide_cyc2	e8eihB1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v295.2)
A	Polyketide_cyc2	e8eihA1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	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, C, D, E	PF00855	PWWP domain (PWWP)	PWWP domain	The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif [1]. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic c ...	The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif [1]. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyses all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organising higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression [2].	Domain
A, B, C, D, E	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
A, B, C, D, E	PF00145	C-5 cytosine-specific DNA methylase (DNA_methylase)	C-5 cytosine-specific DNA methylase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	DNA (cytosine-5)-methyltransferase 3B	DNA binding binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates transferase activity methyltransferase activity DNA binding binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity	regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive 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 transcription by RNA polymerase II 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	protein-containing complex catalytic complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
A, B, C, D, E	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D, E	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
A, B, C, D, E	IPR050390	DNA Cytosine-5 Methyltransferase	Family
A, B, C, D, E	IPR000313	PWWP domain	Domain
A, B, C, D, E	IPR030488	DNA (cytosine-5)-methyltransferase 3B, ADD domain	Domain
A, B, C, D, E	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A, B, C, D, E	IPR001525	C-5 cytosine methyltransferase	Family
A, B, C, D, E	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, C, D, E	IPR025766	ADD domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E	: Q9UBC3	immunodeficiency-centromeric instability-facial anomalies syndrome 1 primary immunodeficiency disease breast carcinoma facioscapulohumeral muscular dystrophy 2 Craniofacial Abnormalities prostate cancer sarcomatoid carcinoma carcinoma immunodeficiency-centromeric instability-facial anomalies syndrome intellectual disability lung adenocarcinoma medulloblastoma non-small cell lung carcinoma autism spectrum disorder schizophrenia immunodeficiency-centromeric instability-facial anomalies syndrome 1 primary immunodeficiency disease breast carcinoma facioscapulohumeral muscular dystrophy 2 Craniofacial Abnormalities prostate cancer sarcomatoid carcinoma carcinoma immunodeficiency-centromeric instability-facial anomalies syndrome intellectual disability lung adenocarcinoma medulloblastoma non-small cell lung carcinoma autism spectrum disorder schizophrenia hereditary diffuse gastric adenocarcinoma invasive ductal breast carcinoma malignant mesothelioma ovarian cancer primitive neuroectodermal tumor cancer undifferentiated carcinoma gastric cancer inflammatory bowel disease large cell medulloblastoma nicotine dependence polycystic ovary syndrome atypical teratoid rhabdoid tumor breast cancer gastric neoplasm