5FWJ | pdb_00005fwj

Crystal structure of human JARID1C in complex with KDM5-C49

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)
B	d5fwjb1	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	Jumonji domain / Histone demethylase core	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5fwjb2	Small proteins	Jumonji C-terminal domain-like	Jumonji C-terminal domain-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5fwjb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5fwja1	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	Jumonji domain / Histone demethylase core	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5fwja2	Small proteins	Jumonji C-terminal domain-like	Jumonji C-terminal domain-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5fwja3	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
B		e5fwjB1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: Asp_Arg_Hydrox	F:	ECOD (20:10:01)
A		e5fwjA1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: Asp_Arg_Hydrox	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
A	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21323	Lysine-specific demethylase 5, C-terminal helical domain (KDM5_C-hel)	Lysine-specific demethylase 5, C-terminal helical domain	This is the C-terminal helical domain from Lysine-specific demethylase 5 subfamily (KDM5), which is localised between the Jumonji C (JmjC) domain and the C5HC2 zinc finger motif (Pfam:PF02928) [1-5].	Domain
A, B	PF02928	C5HC2 zinc finger (zf-C5HC2)	C5HC2 zinc finger	Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji [1]. This domain may have a DNA binding function.	Domain
A, B	PF02373	JmjC domain, hydroxylase (JmjC)	JmjC domain, hydroxylase	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the ...	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	HISTONE DEMETHYLASE JARID1C	DNA binding binding nucleic acid binding catalytic activity, acting on a protein protein demethylase activity histone H3 demethylase activity histone modifying activity histone demethylase activity catalytic activity demethylase activity histone H3K4 demethylase activity cation binding transition metal ion binding zinc ion binding DNA binding binding nucleic acid binding catalytic activity, acting on a protein protein demethylase activity histone H3 demethylase activity histone modifying activity histone demethylase activity catalytic activity demethylase activity histone H3K4 demethylase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone H3K4me/H3K4me2/H3K4me3 demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen dioxygenase activity oxidoreductase activity 2-oxoglutarate-dependent dioxygenase activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process rhythmic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001965	Zinc finger, PHD-type	Domain
A, B	IPR048615	Lysine-specific demethylase 5, C-terminal helical domain	Domain
A, B	IPR003347	JmjC domain	Domain
A, B	IPR003349	JmjN domain	Domain
A, B	IPR001606	ARID DNA-binding domain	Domain
A, B	IPR019787	Zinc finger, PHD-finger	Domain
A, B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A, B	IPR013637	Lysine-specific demethylase-like domain	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR004198	Zinc finger, C5HC2-type	Domain
A, B	IPR036431	ARID DNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P41229	syndromic X-linked intellectual disability Claes-Jensen type intellectual disability renal cell carcinoma autism papillary renal cell carcinoma collecting duct carcinoma chromophobe renal cell carcinoma sarcomatoid renal cell carcinoma clear cell renal carcinoma Mental Retardation, Psychosocial renal carcinoma lung cancer osteosarcoma ovarian cancer psoriasis

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.