Annotations: 8QZM

Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome

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)
H	SCOP2B Superfamily	Core histone-like	8066267	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8066267	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8067130	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8067130	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8070545	3001387	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)
K	AAA	e8qzmK01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA	ECOD (v295)
H	Rnf-Nqr	e8qzmH1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Rnf-Nqr	ECOD (v295)
D	Rnf-Nqr	e8qzmD1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Rnf-Nqr	ECOD (v295)
G	Rnf-Nqr	e8qzmG1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Rnf-Nqr	ECOD (v295)
C	AAA	e8qzmC01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA	ECOD (v295)
F	Rnf-Nqr	e8qzmF1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Rnf-Nqr	ECOD (v295)
B	Rnf-Nqr	e8qzmB1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Rnf-Nqr	ECOD (v295)
E	Rnf-Nqr	e8qzmE1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Rnf-Nqr	ECOD (v295)
A	Rnf-Nqr	e8qzmA1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Rnf-Nqr	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, G	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
B, F	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain
A, E	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
K	DNA (cytosine-5)-methyltransferase 3A	RNA binding binding lncRNA binding nucleic acid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding DNA binding sequence-specific DNA 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 RNA binding binding lncRNA binding nucleic acid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding DNA binding sequence-specific DNA 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 chromatin binding unmethylated CpG binding transcription corepressor activity transcription regulator activity transcription coregulator activity 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 DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid cation binding transition metal ion binding zinc ion binding ion binding metal ion 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 response to stimulus response to chemical response to xenobiotic stimulus negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic 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 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 response to nutrient levels response to lipid response to nutrient response to vitamin A response to vitamin developmental process multicellular organismal process cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development animal gross anatomical part developmental process system development response to toxic substance cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation response to ionizing radiation response to radiation response to metal ion response to lead ion hepatocyte apoptotic process apoptotic process cell death programmed cell death epithelial cell apoptotic process response to alcohol response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to alcohol cellular response to ethanol response to ethanol transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation retrotransposition transposable element silencing by heterochromatin formation transposition transposable element silencing by piRNA-mediated DNA methylation transposable element silencing gene silencing by piRNA-directed DNA methylation piRNA-mediated heterochromatin formation response to nitrogen compound response to cocaine response to alkaloid response to estradiol	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix XY body sex chromosome membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix XY body sex chromosome membraneless organelle intracellular membraneless organelle chromosome chromosome, centromeric region chromosomal region cytoplasm nucleoplasm chromatin heterochromatin euchromatin
J	DNA (145-MER)	-	-	-
I	DNA (145-MER)	-	-	-
D, H	Histone H2B type 1-C/E/F/G/I	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin identical protein binding	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 biological process involved in interspecies interaction between organisms protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 biological process involved in interspecies interaction between organisms innate immune response in mucosa response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus mucosal immune response organ or tissue specific immune response humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide antibacterial humoral response defense response to bacterium response to bacterium defense response to Gram-positive bacterium	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, G	Histone H2A type 1	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity enzyme binding structural molecule activity structural constituent of chromatin	regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization 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 heterochromatin formation epigenetic regulation of gene expression regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization 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 heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B, F	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity RNA binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 organelle organization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 organelle organization telomere organization chromosome organization localization protein localization to chromatin protein localization to chromosome protein localization to chromosome, centromeric region protein localization to organelle macromolecule localization protein localization to CENP-A containing chromatin intracellular protein localization multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process regulation of megakaryocyte differentiation negative regulation of biological process cell development megakaryocyte differentiation regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of biological process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle chromosome, telomeric region chromosomal region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, E	Histone H3 (Fragment)	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
K	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
K	IPR044108	DNA (cytosine-5)-methyltransferase 3A, ADD domain	Domain
K	IPR000313	PWWP domain	Domain
K	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
K	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
K	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
K	IPR050390	DNA Cytosine-5 Methyltransferase	Family
K	IPR001525	C-5 cytosine methyltransferase	Family
K	IPR054724	DNA (cytosine-5)-methyltransferase, N-terminal	Domain
K	IPR025766	ADD domain	Domain
D, H	IPR009072	Histone-fold	Homologous Superfamily
D, H	IPR000558	Histone H2B	Family
D, H	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
D, H	IPR055333	Histone H2B, conserved site	Conserved Site
C, G	IPR009072	Histone-fold	Homologous Superfamily
C, G	IPR002119	Histone H2A	Family
C, G	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C, G	IPR032454	Histone H2A, C-terminal domain	Domain
C, G	IPR032458	Histone H2A conserved site	Conserved Site
B, F	IPR009072	Histone-fold	Homologous Superfamily
B, F	IPR035425	CENP-T/Histone H4, histone fold	Domain
B, F	IPR001951	Histone H4	Family
B, F	IPR019809	Histone H4, conserved site	Conserved Site
B, F	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
A, E	IPR009072	Histone-fold	Homologous Superfamily
A, E	IPR000164	Histone H3/CENP-A	Family
A, E	IPR007125	Core Histone H2A/H2B/H3 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
K	: Q9Y6K1	tall stature-intellectual disability-facial dysmorphism syndrome Crohn disease acute monocytic leukemia juvenile myelomonocytic leukemia acute myeloid leukemia intellectual disability 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 acute myeloid leukemia intellectual disability 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 ductal breast carcinoma in situ non-small cell lung carcinoma genetic endocrine growth disease pancreatic intraductal papillary-mucinous neoplasm primary biliary cholangitis ileocolitis systemic mastocytosis atypical teratoid rhabdoid tumor lung cancer malignant ependymoma congenital anemia Crohn's colitis myelodysplastic syndrome oligodendroglioma glioblastoma hematologic disease large cell medulloblastoma autism spectrum disorder malignant glioma osteosarcoma granulomatous slack skin disease plasma cell myeloma hypertensive disorder primitive neuroectodermal tumor invasive ductal breast carcinoma lung benign neoplasm cancer malignant mesothelioma medulloblastoma
D, H	: P62807	breast carcinoma lung adenocarcinoma breast cancer lung carcinoma Malignant neoplasm of breast ovarian cancer ulcerative colitis autism spectrum disorder exocrine pancreatic carcinoma hypertensive disorder malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma psoriasis allergic rhinitis breast carcinoma lung adenocarcinoma breast cancer lung carcinoma Malignant neoplasm of breast ovarian cancer ulcerative colitis autism spectrum disorder exocrine pancreatic carcinoma hypertensive disorder malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma psoriasis allergic rhinitis cutaneous lupus erythematosus ductal breast carcinoma in situ glioblastoma interstitial cystitis lung cancer malignant mesothelioma osteoarthritis squamous cell lung carcinoma atypical teratoid rhabdoid tumor cystic fibrosis endogenous depression gout invasive ductal breast carcinoma
C, G	: P0C0S8	malignant pancreatic neoplasm ovarian cancer psoriasis acne benign prostatic hyperplasia chronic obstructive pulmonary disease exocrine pancreatic carcinoma glioblastoma lung cancer malignant glioma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast cancer malignant pancreatic neoplasm ovarian cancer psoriasis acne benign prostatic hyperplasia chronic obstructive pulmonary disease exocrine pancreatic carcinoma glioblastoma lung cancer malignant glioma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast cancer cutaneous lupus erythematosus gastric cancer hepatocellular carcinoma lung carcinoma malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm autism spectrum disorder breast carcinoma endogenous depression gastric carcinoma lung adenocarcinoma malignant colon neoplasm
B, F	: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease acute myeloid leukemia squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease acute myeloid leukemia squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pilocytic astrocytoma allergic rhinitis ulcerative colitis autism spectrum disorder cystic fibrosis endogenous depression glioblastoma hypertensive disorder lung cancer malignant mesothelioma multiple sclerosis osteosarcoma psoriasis astrocytic tumor breast cancer diabetes mellitus endometriosis gout invasive ductal breast carcinoma