4CCM | pdb_00004ccm

60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1)

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Hemagglutinin	e4ccmC01	A: alpha bundles	X: Rossmann-like	H: P-loop domains-related	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: Hemagglutinin	ECOD (develop294)
B	Hormone_recep	e4ccmB1	A: alpha bundles	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Hormone_recep	ECOD (develop294)
A	Hormone_recep	e4ccmA1	A: alpha bundles	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Hormone_recep	ECOD (develop294)

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)
B	1.10.10.1500	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	JmjC domain-containing ribosomal oxygenase (ROX), dimer domain	CATH (4.3.0)
B	3.90.930.40	Alpha Beta	Alpha-Beta Complex	Outer Surface Protein A	domain 3	CATH (4.3.0)
A	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
A	1.10.10.1500	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	JmjC domain-containing ribosomal oxygenase (ROX), dimer domain	CATH (4.3.0)
A	3.90.930.40	Alpha Beta	Alpha-Beta Complex	Outer Surface Protein A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21233	Ribosomal oxygenase 1, C-terminal winged helix domain (WHD_RIOX1)	Ribosomal oxygenase 1, C-terminal winged helix domain	This domain is found in Ribosomal oxygenase 1 from humans (RIOX1) and similar proteins from animals. RIOX1 catalyse histidine- hydroxylation in ribosomal protein rpL28. The protein shows a JmjC domain followed by an helical dimerization domain and a ...	This domain is found in Ribosomal oxygenase 1 from humans (RIOX1) and similar proteins from animals. RIOX1 catalyse histidine- hydroxylation in ribosomal protein rpL28. The protein shows a JmjC domain followed by an helical dimerization domain and a C-terminal winged-helix (WH)-domain (this entry) [1,2].	Domain
A, B	PF08007	JmjC domain (JmjC_2)	JmjC domain	This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 [1], Ribosomal oxygenase 1/2 [2,3], and 50S ribosomal protein L16 3-hydroxylase fro ...	This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 [1], Ribosomal oxygenase 1/2 [2,3], and 50S ribosomal protein L16 3-hydroxylase from Escherichia coli [4,5]. Proteins are bifunctional, acting as histone lysine demethylases and ribosomal histidine hydroxylases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	60S RIBOSOMAL PROTEIN L8	RNA binding binding rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane intracellular organelle intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane intracellular organelle intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization synapse asymmetric synapse protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, B	BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66	histone H3K36 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 demethylase activity histone H3K36me/H3K36me2 demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity histone H3K4 demethylase activity histone H3K36 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 demethylase activity histone H3K36me/H3K36me2 demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity histone H3K4 demethylase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding histone H3K4me/H3K4me2/H3K4me3 demethylase activity peptidyl-histidine 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 cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair regulation of cellular response to stress negative regulation of DNA repair regulation of response to stress negative regulation of response to stimulus regulation of DNA repair regulation of response to stimulus negative regulation of DNA metabolic process regulation of DNA metabolic process developmental process regulation of osteoblast differentiation multicellular organismal process regulation of developmental process cellular developmental process negative regulation of osteoblast differentiation negative regulation of developmental process regulation of cell differentiation osteoblast differentiation ossification cell differentiation negative regulation of cell differentiation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR023672	Large ribosomal subunit protein uL2, archaea/eukaryota	Family
C, D	IPR022669	Large ribosomal subunit protein uL2, C-terminal	Domain
C, D	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
C, D	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
C, D	IPR022671	Large ribosomal subunit protein uL2, conserved site	Conserved Site
C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C, D	IPR022666	Large ribosomal subunit protein uL2, RNA-binding domain	Domain
C, D	IPR014726	Large ribosomal subunit protein uL2, domain 3	Homologous Superfamily
C, D	IPR002171	Large ribosomal subunit protein uL2	Family
A, B	IPR049043	RIOX1/NO66-like, C-terminal winged helix domain	Domain
A, B	IPR003347	JmjC domain	Domain
A, B	IPR039994	Histone lysine demethylase/ribosomal histidine hydroxylase NO66-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9H6W3	astrocytic tumor osteosarcoma lung cancer oligodendroglioma

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.

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