5EXH

Crystal structure of mTET3-CXXC domain in complex with 5-carboxylcytosine DNA at 1.3 Angstroms resolution.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	CXXC zinc-finger domain	8053019	4006601	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	CXXC zinc-finger domain	8053020	3002156	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	zf-CXXC	e5exhC1	A: few secondary structure elements	X: CXXC domain-like	H: CXXC domain (From Topology)	T: CXXC domain	F: zf-CXXC	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA (5'-D(GPAPAPTPCP(1CC)PGPGPAPTPTPC)-3')	-	-	-
C	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 sequence-specific DNA binding DNA binding binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding nucleic acid binding heterocyclic compound 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 sequence-specific DNA binding DNA binding binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding nucleic acid binding heterocyclic compound binding methyl-CpG binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA modification organic substance metabolic process DNA demethylation DNA dealkylation macromolecule modification metabolic process demethylation macromolecule metabolic process regulation of cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA modification organic substance metabolic process DNA demethylation DNA dealkylation macromolecule modification metabolic process demethylation macromolecule metabolic process regulation of cellular process epigenetic programming in the zygotic pronuclei cellular biosynthetic process epigenetic programing of male pronucleus protein-DNA complex organization cellular component organization chromatin organization organic substance biosynthetic process chromatin remodeling cellular component organization or biogenesis regulation of biosynthetic process epigenetic programming of gene expression regulation of biological process protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process cellular process regulation of macromolecule biosynthetic process regulation of metabolic process organonitrogen compound catabolic process pyrimidine-containing compound metabolic process organonitrogen compound metabolic process catabolic process pyrimidine-containing compound catabolic process 5-methylcytosine catabolic process organic cyclic compound catabolic process 5-methylcytosine metabolic process organic substance catabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process protein metabolic process protein modification process carbohydrate derivative biosynthetic process glycoprotein biosynthetic process glycoprotein metabolic process protein glycosylation glycosylation macromolecule glycosylation protein O-linked glycosylation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound 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 organic cyclic compound biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	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 membrane-enclosed lumen 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 membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen male pronucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR002857	Zinc finger, CXXC-type	Domain
C	IPR046942	Methylcytosine dioxygenase TET1-3, oxygenase domain	Domain
C	IPR024779	2OGFeDO JBP1/TET, oxygenase domain	Domain
C	IPR040175	Methylcytosine dioxygenase TET1/2/3	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.