8U2Y

Solution structure of the PHD6 finger of MLL4 bound to TET3

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	Methylcytosine dioxygenase TET3	5-methylcytosine dioxygenase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding 5-methylcytosine dioxygenase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region 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 positive regulation of gene expression via chromosomal CpG island demethylation positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II chromatin organization positive regulation of macromolecule metabolic process transcription initiation at RNA polymerase II promoter regulation of biological process cellular metabolic process regulation of cellular metabolic process regulation of cellular process positive regulation of gene expression via chromosomal CpG island demethylation positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II chromatin organization positive regulation of macromolecule metabolic process transcription initiation at RNA polymerase II promoter regulation of biological process cellular metabolic process regulation of cellular metabolic process primary metabolic process regulation of gene expression biosynthetic process transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process protein-DNA complex organization cellular component organization RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process chromatin remodeling cellular component organization or biogenesis positive regulation of cellular process regulation of biosynthetic process protein-containing complex organization epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of cellular biosynthetic process positive regulation of gene expression cellular process positive regulation of cellular biosynthetic process epigenetic programming in the zygotic pronuclei epigenetic programing of male pronucleus epigenetic programming of gene expression organonitrogen compound catabolic process pyrimidine-containing compound metabolic process organonitrogen compound metabolic process catabolic process pyrimidine-containing compound catabolic process 5-methylcytosine catabolic process 5-methylcytosine metabolic process carbohydrate derivative biosynthetic process organonitrogen compound biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process glycoprotein metabolic process protein glycosylation glycosylation macromolecule modification macromolecule glycosylation protein O-linked glycosylation protein metabolic process protein modification process positive regulation of DNA-templated transcription regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle female pronucleus nucleus pronucleus intracellular membrane-bounded organelle cytoplasm male pronucleus
B	Histone-lysine N-methyltransferase 2D	protein binding binding histone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein binding binding histone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K4 methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity histone H3K4 trimethyltransferase activity histone H3K4 monomethyltransferase activity cation binding ion binding metal ion binding small molecule binding	developmental process sexual reproduction cellular developmental process reproductive process oogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism female gamete generation developmental process involved in reproduction gamete generation cell differentiation anatomical structure development germ cell development developmental process sexual reproduction cellular developmental process reproductive process oogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism female gamete generation developmental process involved in reproduction gamete generation cell differentiation anatomical structure development germ cell development cellular process response to stimulus response to hormone response to endogenous stimulus response to chemical response to estrogen cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis beta-catenin-TCF complex assembly methylation metabolic process regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of cellular process developmental cell growth developmental growth growth cell growth oocyte development oocyte growth oocyte differentiation cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction intracellular receptor signaling pathway response to lipid signaling positive regulation of intracellular estrogen receptor signaling pathway regulation of signal transduction hormone-mediated signaling pathway intracellular signal transduction cell communication positive regulation of response to stimulus cellular response to endogenous stimulus regulation of intracellular signal transduction response to steroid hormone regulation of intracellular estrogen receptor signaling pathway regulation of intracellular steroid hormone receptor signaling pathway signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus response to organic cyclic compound steroid hormone receptor signaling pathway cellular response to hormone stimulus regulation of signaling cellular response to organic cyclic compound positive regulation of intracellular signal transduction estrogen receptor signaling pathway positive regulation of intracellular steroid hormone receptor signaling pathway cellular response to chemical stimulus regulation of response to stimulus cellular response to lipid regulation of cell communication nuclear receptor-mediated signaling pathway positive regulation of signaling positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane-bounded organelle MLL3/4 complex protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex intracellular organelle lumen intracellular organelle membrane-bounded organelle MLL3/4 complex protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002857	Zinc finger, CXXC-type	Domain
A	IPR046942	Methylcytosine dioxygenase TET1-3, oxygenase domain	Domain
A	IPR024779	2OGFeDO JBP1/TET, oxygenase domain	Domain
A	IPR040175	Methylcytosine dioxygenase TET1/2/3	Family
B	IPR037890	KMT2D, SET domain	Domain
B	IPR001965	Zinc finger, PHD-type	Domain
B	IPR046341	SET domain superfamily	Homologous Superfamily
B	IPR047000	KMT2D, PHD3 domain	Domain
B	IPR001214	SET domain	Domain
B	IPR019787	Zinc finger, PHD-finger	Domain
B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B	IPR041964	KMT2D, ePHD2 domain	Domain
B	IPR003616	Post-SET domain	Domain
B	IPR034732	Extended PHD (ePHD) domain	Domain
B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B	IPR003889	FY-rich, C-terminal	Conserved Site
B	IPR041961	KMT2D, ePHD1 domain	Domain
B	IPR046999	KMT2D, PHD5 domain	Domain
B	IPR003888	FY-rich, N-terminal	Conserved Site
B	IPR001841	Zinc finger, RING-type	Domain
B	IPR009071	High mobility group box domain	Domain
B	IPR036910	High mobility group box domain superfamily	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.

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8U2Y

Solution structure of the PHD6 finger of MLL4 bound to TET3

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage