8U5H

Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome

External Resource: Annotation

Domain Annotation: SCOP2 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)
D	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2021-05-27)
F [auth I]	SCOP2B Superfamily	Core histone-like	8070525	3001387	SCOP2B (2021-05-27)
J [auth O]	SCOP2B Superfamily	Core histone-like	8070525	3001387	SCOP2B (2021-05-27)
L [auth R]	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2021-05-27)
H [auth K]	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2021-05-27)
I [auth M]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2021-05-27)
M [auth S]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2021-05-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
H [auth K], L [auth R]	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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 chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis 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 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 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 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 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 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 regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA 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 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	nucleosome DNA	-	-	-
D	Ubiquitin	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding RNA binding organic cyclic compound binding nucleic acid binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process protein ubiquitination organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
E [auth H]	nucleosome DNA	-	-	-
F [auth I], J [auth O]	Histone H3.3C	DNA binding binding organic cyclic compound 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 chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
G [auth J], K [auth Q]	Histone H4	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding 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	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
H [auth K], L [auth R]	Histone H2A	DNA binding binding organic cyclic compound 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 chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
I [auth M], M [auth S]	Histone H2B 1.1	DNA binding binding organic cyclic compound 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 chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
A, B	IPR044108	DNA (cytosine-5)-methyltransferase 3A, ADD domain	Domain
A, B	IPR000313	PWWP domain	Domain
A, B	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A, B	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
A, B	IPR001525	C-5 cytosine methyltransferase	Family
A, B	IPR025766	ADD domain	Domain
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
D	IPR019954	Ubiquitin conserved site	Conserved Site
D	IPR000626	Ubiquitin-like domain	Domain
D	IPR019956	Ubiquitin domain	Domain
D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
F [auth I], J [auth O]	IPR009072	Histone-fold	Homologous Superfamily
F [auth I], J [auth O]	IPR007125	Histone H2A/H2B/H3	Domain
F [auth I], J [auth O]	IPR000164	Histone H3/CENP-A	Family
G [auth J], K [auth Q]	IPR009072	Histone-fold	Homologous Superfamily
G [auth J], K [auth Q]	IPR001951	Histone H4	Family
G [auth J], K [auth Q]	IPR035425	CENP-T/Histone H4, histone fold	Domain
G [auth J], K [auth Q]	IPR019809	Histone H4, conserved site	Conserved Site
G [auth J], K [auth Q]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
H [auth K], L [auth R]	IPR009072	Histone-fold	Homologous Superfamily
H [auth K], L [auth R]	IPR007125	Histone H2A/H2B/H3	Domain
H [auth K], L [auth R]	IPR002119	Histone H2A	Family
H [auth K], L [auth R]	IPR032454	Histone H2A, C-terminal domain	Domain
H [auth K], L [auth R]	IPR032458	Histone H2A conserved site	Conserved Site
I [auth M], M [auth S]	IPR009072	Histone-fold	Homologous Superfamily
I [auth M], M [auth S]	IPR007125	Histone H2A/H2B/H3	Domain
I [auth M], M [auth S]	IPR000558	Histone H2B	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	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 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 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 granulomatous slack skin disease plasma cell myeloma hypertensive disorder primitive neuroectodermal tumor invasive ductal breast carcinoma lung benign neoplasm malignant mesothelioma cancer medulloblastoma
D	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer