8SKZ

Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome

External Resource: Annotation

Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity ATP-dependent chromatin remodeler activity chromatin binding	DNA-mediated transformation horizontal gene transfer cellular process transposition retrotransposition regulation of cellular process negative regulation of biological process 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 DNA-mediated transformation horizontal gene transfer cellular process transposition retrotransposition regulation of cellular process negative regulation of biological process 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 heterochromatin formation 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 macromolecule metabolic process regulation of metabolic process constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression via chromosomal CpG island methylation cell division apoptotic process cell death programmed cell death pericentric heterochromatin formation developmental process multicellular organism development multicellular organismal process anatomical structure development urogenital system development system development cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway signal transduction intrinsic apoptotic signaling pathway regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process negative regulation of signal transduction negative regulation of intrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of cell communication regulation of apoptotic signaling pathway cell population proliferation immune system process mononuclear cell proliferation lymphocyte proliferation cell activation lymphocyte activation leukocyte proliferation leukocyte activation animal organ development kidney development renal system development response to peptide response to chemical response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor	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 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 chromosome, centromeric region chromosomal region pericentric heterochromatin heterochromatin
B, E	Histone H3.2	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 intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus membrane-enclosed lumen 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 membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, G	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 intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
D, H	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 intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
F, I	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 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	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
J	DNA (192-MER)	-	-	-
K	DNA (192-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000330	SNF2, N-terminal	Domain
A	IPR044753	HELLS, N-terminal	Domain
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR000330	SNF2, N-terminal	Domain
A	IPR044753	HELLS, N-terminal	Domain
A	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
B, E	IPR009072	Histone-fold	Homologous Superfamily
B, E	IPR007125	Histone H2A/H2B/H3	Domain
B, E	IPR000164	Histone H3/CENP-A	Family
C, G	IPR009072	Histone-fold	Homologous Superfamily
C, G	IPR007125	Histone H2A/H2B/H3	Domain
C, G	IPR002119	Histone H2A	Family
C, G	IPR032454	Histone H2A, C-terminal domain	Domain
C, G	IPR032458	Histone H2A conserved site	Conserved Site
D, H	IPR009072	Histone-fold	Homologous Superfamily
D, H	IPR007125	Histone H2A/H2B/H3	Domain
D, H	IPR000558	Histone H2B	Family
F, I	IPR009072	Histone-fold	Homologous Superfamily
F, I	IPR001951	Histone H4	Family
F, I	IPR035425	CENP-T/Histone H4, histone fold	Domain
F, I	IPR019809	Histone H4, conserved site	Conserved Site
F, I	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NRZ9	immunodeficiency-centromeric instability-facial anomalies syndrome 4 polycystic ovary syndrome Liver Cirrhosis, Experimental immunodeficiency-centromeric instability-facial anomalies syndrome malignant mesothelioma nasopharyngeal carcinoma ovarian cancer pilocytic astrocytoma psoriasis ulcerative colitis atypical teratoid rhabdoid tumor ductal breast carcinoma in situ gastric carcinoma malignant ependymoma malignant pancreatic neoplasm immunodeficiency-centromeric instability-facial anomalies syndrome 4 polycystic ovary syndrome Liver Cirrhosis, Experimental immunodeficiency-centromeric instability-facial anomalies syndrome malignant mesothelioma nasopharyngeal carcinoma ovarian cancer pilocytic astrocytoma psoriasis ulcerative colitis atypical teratoid rhabdoid tumor ductal breast carcinoma in situ gastric carcinoma malignant ependymoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma adrenal cortex carcinoma breast cancer endometriosis glioblastoma invasive ductal breast carcinoma lung adenocarcinoma malignant glioma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor Sjogren syndrome atopic eczema gastric cancer large cell medulloblastoma lung cancer

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 R01GM157729.

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8SKZ

Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation