Annotations: 6A57

Structure of histone demethylase REF6 complexed with DNA

External Resource: Annotation

Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Lsr2_DNA-bd (DEPRECATED)	e6a57A1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lsr2_DNA-bd (DEPRECATED)	ECOD (v295.2)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	DNA (5'-D(GPGPAPCPAPAPAPAPCPAPGPAPGPAPAPA)-3')	-	-	-
B	DNA (5'-D(CPTPTPTPCPTPCPTPGPTPTPTPTPGPTPC)-3')	-	-	-
A	Lysine-specific demethylase REF6	sequence-specific DNA binding DNA binding binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity demethylase activity dioxygenase activity sequence-specific DNA binding DNA binding binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity histone H3K27me2/H3K27me3 demethylase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone H3K4me/H3K4me2/H3K4me3 demethylase activity histone H3K4 demethylase activity	photoperiodism, flowering developmental process response to light stimulus multicellular organismal process regulation of biological process reproductive system development response to stimulus reproductive process biological regulation vegetative to reproductive phase transition of meristem developmental process involved in reproduction multicellular organism development photoperiodism regulation of response to stimulus anatomical structure development photoperiodism, flowering developmental process response to light stimulus multicellular organismal process regulation of biological process reproductive system development response to stimulus reproductive process biological regulation vegetative to reproductive phase transition of meristem developmental process involved in reproduction multicellular organism development photoperiodism regulation of response to stimulus anatomical structure development reproductive structure development post-embryonic development response to radiation response to abiotic stimulus regulation of photoperiodism, flowering system development heat acclimation response to stress response to heat response to temperature stimulus regulation of developmental process positive regulation of biological process post-embryonic root development positive regulation of developmental process regulation of lateral root development regulation of post-embryonic root development lateral root development regulation of multicellular organismal process regulation of root development root development regulation of multicellular organismal development plant organ development plant gross anatomical part developmental process regulation of post-embryonic development positive regulation of multicellular organismal process post-embryonic plant organ development positive regulation of post-embryonic development positive regulation of lateral root development root system development response to lipid response to hormone response to brassinosteroid response to chemical response to endogenous stimulus response to oxygen-containing compound cellular response to stimulus regulation of cellular process signaling cellular response to oxygen-containing compound cell communication sugar mediated signaling pathway cellular response to carbohydrate stimulus cellular response to chemical stimulus response to carbohydrate cellular process signal transduction carbohydrate mediated signaling regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process anatomical structure morphogenesis developmental growth unidimensional cell growth growth cell morphogenesis cell growth developmental growth involved in morphogenesis isoprenoid catabolic process catabolic process alcohol catabolic process oxoacid metabolic process apocarotenoid catabolic process alcohol metabolic process abscisic acid metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process tertiary alcohol metabolic process sesquiterpenoid catabolic process lipid catabolic process sesquiterpenoid metabolic process carboxylic acid metabolic process primary metabolic process terpenoid catabolic process abscisic acid catabolic process olefinic compound catabolic process olefinic compound metabolic process monocarboxylic acid metabolic process small molecule catabolic process terpenoid metabolic process isoprenoid metabolic process lipid metabolic process localization protein localization to chromatin protein localization to chromosome protein localization to organelle macromolecule localization protein localization to heterochromatin intracellular protein localization abscisic acid-activated signaling pathway hormone-mediated signaling pathway cellular response to endogenous stimulus cellular response to hormone stimulus cellular response to abscisic acid stimulus response to abscisic acid response to alcohol cellular response to alcohol cellular response to lipid epigenetic regulation of gene expression cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis RNA metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process response to diterpene regulation of signal transduction intracellular signal transduction regulation of phosphorelay signal transduction system regulation of ethylene-activated signaling pathway regulation of intracellular signal transduction ethylene-activated signaling pathway response to ethylene regulation of signaling phosphorelay signal transduction system cellular response to ethylene stimulus regulation of cell communication response to mechanical stimulus response to external stimulus regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription leaf development shoot system development phyllome development multicellular organismal reproductive process developmental maturation seed dormancy process fruit development seed development release of seed from dormancy exit from dormancy dormancy process seed maturation cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization systemic acquired resistance biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to biotic stimulus defense response to other organism response to external biotic stimulus	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle SWI/SNF superfamily-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle SWI/SNF superfamily-type complex INO80-type complex catalytic complex intracellular membraneless organelle chromatin intracellular membrane-bounded organelle Ino80 complex organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013087	Zinc finger C2H2-type	Domain
A	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A	IPR003347	JmjC domain	Domain
A	IPR003349	JmjN domain	Domain

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

6A57 | pdb_00006a57

Structure of histone demethylase REF6 complexed with DNA

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage