Annotations: 12OG

Cryo-EM structure of Arabidopsis VIM1 in complex with hemi-methylated CG-containing nucleosome 2

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
K [auth M]	DNA	-	-	-
J [auth L]	DNA	-	-	-
I [auth A]	E3 ubiquitin-protein ligase ORTHRUS 2	protein binding binding histone binding DNA binding double-stranded DNA binding double-stranded methylated DNA binding nucleic acid binding chromatin binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity protein binding binding histone binding DNA binding double-stranded DNA binding double-stranded methylated DNA binding nucleic acid binding chromatin binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity nucleoside phosphate binding nucleotide binding methyl-CpNpG binding heterocyclic compound binding small molecule binding sequence-specific DNA binding methyl-CpG binding methyl-CpNpN 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 cell division cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization pericentric heterochromatin formation constitutive heterochromatin formation primary metabolic process protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromocenter membrane-bounded organelle nucleus intracellular membrane-bounded organelle
G [auth H], H [auth I]	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 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
E [auth F], F [auth G]	Histone H3.2	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 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 [auth D], D [auth E]	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
A [auth B], B [auth C]	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth A]	IPR015947	PUA-like superfamily	Homologous Superfamily
I [auth A]	IPR001965	Zinc finger, PHD-type	Domain
I [auth A]	IPR003105	SRA-YDG	Domain
I [auth A]	IPR019787	Zinc finger, PHD-finger	Domain
I [auth A]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
I [auth A]	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
I [auth A]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
I [auth A]	IPR027370	Zinc finger, RING-type, eukaryotic	Domain
I [auth A]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
I [auth A]	IPR047529	E3 ubiquitin-protein ligase ORTHRUS 1-5, second RING finger, HC subclass	Domain
I [auth A]	IPR047498	E3 ubiquitin-protein ligase ORTHRUS 1/2-like, first RING finger, HC subclass	Domain
I [auth A]	IPR045134	UHRF1/2-like	Family
I [auth A]	IPR001841	Zinc finger, RING-type	Domain
I [auth A]	IPR036987	SRA-YDG superfamily	Homologous Superfamily
G [auth H], H [auth I]	IPR009072	Histone-fold	Homologous Superfamily
G [auth H], H [auth I]	IPR001951	Histone H4	Family
G [auth H], H [auth I]	IPR035425	CENP-T/Histone H4, histone fold	Domain
G [auth H], H [auth I]	IPR019809	Histone H4, conserved site	Conserved Site
G [auth H], H [auth I]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
E [auth F], F [auth G]	IPR009072	Histone-fold	Homologous Superfamily
E [auth F], F [auth G]	IPR000164	Histone H3/CENP-A	Family
E [auth F], F [auth G]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C [auth D], D [auth E]	IPR009072	Histone-fold	Homologous Superfamily
C [auth D], D [auth E]	IPR000558	Histone H2B	Family
C [auth D], D [auth E]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C [auth D], D [auth E]	IPR055333	Histone H2B, conserved site	Conserved Site
A [auth B], B [auth C]	IPR009072	Histone-fold	Homologous Superfamily
A [auth B], B [auth C]	IPR002119	Histone H2A	Family
A [auth B], B [auth C]	IPR032454	Histone H2A, C-terminal domain	Domain
A [auth B], B [auth C]	IPR032458	Histone H2A conserved site	Conserved Site
A [auth B], B [auth C]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A [auth B], B [auth C]	IPR061508	Histone H2A, histone fold	Domain

12OG | pdb_000012og

Cryo-EM structure of Arabidopsis VIM1 in complex with hemi-methylated CG-containing nucleosome 2

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage