8WH5

Structure of DDM1-nucleosome complex in the apo state

External Resource: Annotation

Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E	Histone H3.1	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	-	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle extracellular region intracellular non-membrane-bounded organelle non-membrane-bounded organelle chromocenter cytosol cell periphery membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle extracellular region intracellular non-membrane-bounded organelle non-membrane-bounded organelle chromocenter cytosol cell periphery plasma membrane membrane protein-containing complex protein-DNA complex nucleosome chromatin chromosome nucleus
B, F	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	response to acid chemical response to stimulus response to stress response to chemical response to oxygen-containing compound response to abiotic stimulus response to water response to water deprivation response to inorganic substance	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle plastid cytoplasm extracellular region peroxisome microbody cytosol cell periphery plasma membrane membrane cell-cell junction symplast anchoring junction cell junction plasmodesma protein-containing complex protein-DNA complex nucleosome chromatin chromosome chloroplast plant-type vacuole vacuole thylakoid
C, G	Histone H2A.6	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	DNA-mediated transformation horizontal gene transfer cellular process response to stimulus response to stress response to wounding biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle plastid cytoplasm protein-containing complex protein-DNA complex nucleosome chromatin chromosome
D, H	Histone H2B.6	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	-	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle plastid plastid thylakoid chloroplast thylakoid thylakoid chloroplast protein-containing complex protein-DNA complex nucleosome chromatin chromosome plastid stroma chloroplast stroma
I	DNA (sense strand)	-	-	-
J	DNA (antisense strand)	-	-	-
K	ATP-dependent DNA helicase DDM1	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	DNA-mediated transformation horizontal gene transfer cellular process transposition retrotransposition regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process DNA-mediated transformation horizontal gene transfer cellular process transposition retrotransposition regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process 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 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 macromolecule metabolic process regulation of metabolic process DNA methylation-dependent heterochromatin formation facultative heterochromatin formation	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, E	IPR009072	Histone-fold	Homologous Superfamily
A, E	IPR007125	Histone H2A/H2B/H3	Domain
A, E	IPR000164	Histone H3/CENP-A	Family
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
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
K	IPR000330	SNF2, N-terminal	Domain
K	IPR044753	HELLS, N-terminal	Domain
K	IPR001650	Helicase, C-terminal domain-like	Domain
K	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
K	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
K	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
K	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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 R01GM133198.

Prepare Data

Validate Data

Deposit Data

Help and Resources

8WH5

Structure of DDM1-nucleosome complex in the apo state

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage