Annotations: 9Z07

Cryo-EM structure of DNMT1 in complex with unmethylated nucleosome core particle

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)
K [auth q]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
E [auth Q]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
J [auth p]	SCOP2B Superfamily	Core histone-like	8096712	3001387	SCOP2B (2022-06-29)
D [auth P]	SCOP2B Superfamily	Core histone-like	8096712	3001387	SCOP2B (2022-06-29)
I [auth o]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
C [auth O]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
H [auth n]	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
B [auth N]	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	BAH domain	8053032	3001462	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	BAH domain	8053033	3001462	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053034	3000118	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth Q], K [auth q]	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
D [auth P], J [auth p]	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
B [auth N], H [auth n]	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
A	PF01426	BAH domain (BAH)	BAH domain	This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction [3].	Domain
A	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
G [auth Y]	Chain Y DNA (149-MER)	-	-	-
F [auth X]	Chain x DNA (149-MER)	-	-	-
E [auth Q], K [auth q]	Histone H4	DNA binding 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 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 regulation of cellular process 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 regulation of cellular process negative regulation of biological process negative regulation of cellular process 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 negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	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
D [auth P], J [auth p]	Histone H3	DNA binding protein-containing complex binding binding chromatin binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding protein heterodimerization activity protein binding protein dimerization activity 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	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
C [auth O], I [auth o]	Histone H2B 1.1	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	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 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 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 antibacterial humoral response defense response to bacterium response to bacterium	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
B [auth N], H [auth n]	Histone H2A	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity 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	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
A	DNA (cytosine-5)-methyltransferase 1	RNA binding binding lncRNA binding nucleic acid binding DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity RNA binding binding lncRNA binding nucleic acid binding DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity histone H3K18ub reader activity molecular adaptor activity chromatin binding promoter-specific chromatin binding DNA binding histone H3K14ub reader activity DNA (cytosine-5-)-methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone H3K23ub reader activity sequence-specific DNA binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	regulation of cellular process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation 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 epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of cellular process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation 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 epigenetic regulation of gene expression negative regulation of metabolic process biological regulation 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 negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process negative regulation of phenotypic switching regulation of phenotypic switching phenotypic switching regulation of vascular associated smooth muscle cell proliferation cell population proliferation positive regulation of vascular associated smooth muscle cell proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation chromosomal DNA methylation maintenance following DNA replication muscle cell apoptotic process smooth muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cell death regulation of smooth muscle cell apoptotic process negative regulation of vascular associated smooth muscle cell apoptotic process vascular associated smooth muscle cell apoptotic process negative regulation of smooth muscle cell apoptotic process negative regulation of apoptotic process negative regulation of muscle cell apoptotic process regulation of vascular associated smooth muscle cell apoptotic process apoptotic process programmed cell death multicellular organismal process smooth muscle cell differentiation regulation of developmental process cellular developmental process regulation of smooth muscle cell differentiation negative regulation of muscle cell differentiation regulation of cell differentiation muscle cell differentiation muscle structure development multicellular organism development vascular associated smooth muscle cell differentiation cell differentiation anatomical structure development negative regulation of cell differentiation system development developmental process negative regulation of developmental process negative regulation of vascular associated smooth muscle cell differentiation regulation of vascular associated smooth muscle cell differentiation vasculature development circulatory system development negative regulation of smooth muscle cell differentiation regulation of muscle cell differentiation animal gross anatomical part developmental 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 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	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen pericentric heterochromatin intracellular membraneless organelle chromatin chromosome heterochromatin chromosomal region membraneless organelle chromosome, centromeric region replication fork

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth Q], K [auth q]	IPR009072	Histone-fold	Homologous Superfamily
E [auth Q], K [auth q]	IPR001951	Histone H4	Family
E [auth Q], K [auth q]	IPR035425	CENP-T/Histone H4, histone fold	Domain
E [auth Q], K [auth q]	IPR019809	Histone H4, conserved site	Conserved Site
E [auth Q], K [auth q]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
D [auth P], J [auth p]	IPR009072	Histone-fold	Homologous Superfamily
D [auth P], J [auth p]	IPR000164	Histone H3/CENP-A	Family
D [auth P], J [auth p]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C [auth O], I [auth o]	IPR009072	Histone-fold	Homologous Superfamily
C [auth O], I [auth o]	IPR000558	Histone H2B	Family
C [auth O], I [auth o]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C [auth O], I [auth o]	IPR055333	Histone H2B, conserved site	Conserved Site
B [auth N], H [auth n]	IPR009072	Histone-fold	Homologous Superfamily
B [auth N], H [auth n]	IPR002119	Histone H2A	Family
B [auth N], H [auth n]	IPR032454	Histone H2A, C-terminal domain	Domain
B [auth N], H [auth n]	IPR032458	Histone H2A conserved site	Conserved Site
B [auth N], H [auth n]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B [auth N], H [auth n]	IPR061508	Histone H2A, histone fold	Domain
A	IPR001025	Bromo adjacent homology (BAH) domain	Domain
A	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A	IPR002857	Zinc finger, CXXC-type	Domain
A	IPR022702	DNA (cytosine-5)-methyltransferase 1, replication foci domain	Domain
A	IPR031303	DNA methylase, C-5 cytosine-specific, conserved site	Conserved Site
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR010506	DMAP1-binding domain	Domain
A	IPR043151	Bromo adjacent homology (BAH) domain superfamily	Homologous Superfamily
A	IPR050390	DNA Cytosine-5 Methyltransferase	Family
A	IPR001525	C-5 cytosine methyltransferase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: P26358	hereditary sensory neuropathy-deafness-dementia syndrome medulloblastoma tubular adenocarcinoma carcinoma melanotic medulloblastoma hearing loss disorder prostate cancer hereditary sensory and autonomic neuropathy type 4 sarcomatoid carcinoma breast carcinoma Charcot-Marie-Tooth disease malignant colon neoplasm Clear-cell metastatic renal cell carcinoma adenocarcinoma prostate intraepithelial neoplasia hereditary sensory neuropathy-deafness-dementia syndrome medulloblastoma tubular adenocarcinoma carcinoma melanotic medulloblastoma hearing loss disorder prostate cancer hereditary sensory and autonomic neuropathy type 4 sarcomatoid carcinoma breast carcinoma Charcot-Marie-Tooth disease malignant colon neoplasm Clear-cell metastatic renal cell carcinoma adenocarcinoma prostate intraepithelial neoplasia childhood medulloblastoma dementia medullomyoblastoma with myogenic differentiation adult medulloblastoma granular cell carcinoma peripheral neuropathy asthma autosomal dominant cerebellar ataxia, deafness and narcolepsy breast cancer invasive ductal breast carcinoma lymphoplasmacytic lymphoma chronic myelomonocytic leukemia acute myeloid leukemia cribriform carcinoma dermatomyositis gastric cancer myopathy pancreatic intraductal papillary-mucinous neoplasm hereditary sensory and autonomic neuropathy psoriasis astrocytic tumor benign colon neoplasm ulcerative colitis juvenile dermatomyositis cribriform carcinoma of breast adrenal cortex carcinoma desmoplastic/nodular medulloblastoma anxiety disorder gastric neoplasm peripheral nervous system disease hematologic disease hereditary sensory and autonomic neuropathy type 1 rheumatoid arthritis hereditary sensory and autonomic neuropathy type 5 schizophrenia bipolar disorder sensory peripheral neuropathy cancer intellectual disability undifferentiated carcinoma Kleine-Levin syndrome malignant mesothelioma colonic neoplasm myelodysplastic syndrome ovarian cancer hereditary diffuse gastric adenocarcinoma hereditary sensory and autonomic neuropathy type 2 Riley-Day syndrome