2XDP | pdb_00002xdp

Crystal structure of the tudor domain of human JMJD2C

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2xdpa1	All beta proteins	SH3-like barrel	Tudor/PWWP/MBT	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	LBR_tudor_1	e2xdpA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LBR_tudor_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	3.10.330.70	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18104	Jumonji domain-containing protein 2A Tudor domain (Tudor_2)	Jumonji domain-containing protein 2A Tudor domain	This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means o ...	This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms [3]. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD) [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	LYSINE-SPECIFIC DEMETHYLASE 4C	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding DNA-binding transcription factor binding nuclear androgen receptor binding histone H3K9me2/H3K9me3 demethylase activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone H3K9 demethylase activity histone demethylase activity demethylase activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding DNA-binding transcription factor binding nuclear androgen receptor binding histone H3K9me2/H3K9me3 demethylase activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone H3K9 demethylase activity histone demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity histone H3K36 demethylase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding enzyme binding	developmental process multicellular organismal process chordate embryonic development embryo development in utero embryonic development multicellular organism development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching anatomical structure development anatomical structure formation involved in morphogenesis blastocyst development regulation of biological process regulation of cellular process developmental process multicellular organismal process chordate embryonic development embryo development in utero embryonic development multicellular organism development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching anatomical structure development anatomical structure formation involved in morphogenesis blastocyst development regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process cellular response to stimulus intracellular receptor signaling pathway response to stimulus response to lipid signaling hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone androgen receptor signaling pathway signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus cellular response to chemical stimulus response to chemical cellular response to lipid nuclear receptor-mediated signaling pathway regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of biological process positive regulation of cellular process maintenance of cell number stem cell population maintenance regulation of signal transduction regulation of intracellular signal transduction regulation of intracellular steroid hormone receptor signaling pathway regulation of signaling regulation of androgen receptor signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule 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 primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome pericentric heterochromatin heterochromatin chromosomal region chromosome, centromeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR002999	Tudor domain	Domain
A	IPR003347	JmjC domain	Domain
A	IPR003349	JmjN domain	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR034732	Extended PHD (ePHD) domain	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR040477	Lysine-specific demethylase 4-like, Tudor domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9H3R0	medulloblastoma adult medulloblastoma medullomyoblastoma with myogenic differentiation melanotic medulloblastoma childhood medulloblastoma desmoplastic/nodular medulloblastoma large cell medulloblastoma psoriasis alcohol withdrawal glioblastoma malignant mesothelioma immunodeficiency 31B ovarian cancer

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.