9F81 | pdb_00009f81

Crystal structure of RIOK2 with a covalent compound GCL 47

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
B [auth G]	WD40	e9f81G1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
A	WD40	e9f81A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth G]	PF09202	Rio2, N-terminal (Rio2_N)	Rio2, N-terminal	Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding ...	Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains [1].	Domain
A, B [auth G]	PF01163	RIO domain (RIO1)	RIO domain	This is the atypical serine kinase domain found in RIO family of proteins and related sequences, which is conserved in archaea, bacteria and eukaryotes [5,6]. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, ...	This is the atypical serine kinase domain found in RIO family of proteins and related sequences, which is conserved in archaea, bacteria and eukaryotes [5,6]. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined [4]. This domain is also found at the C-terminal of EKC/KEOPS complex subunit BUD32 from Fungi and Kae1/Bud32 from archaea [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth G]	Serine/threonine-protein kinase RIO2	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine/threonine kinase activity cation binding metal ion binding protein serine kinase activity	regulation of chromosome segregation regulation of cell cycle phase transition regulation of cellular process regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle cell cycle cellular component organization or biogenesis regulation of cell cycle chromosome segregation regulation of chromosome segregation regulation of cell cycle phase transition regulation of cellular process regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle cell cycle cellular component organization or biogenesis regulation of cell cycle chromosome segregation cell cycle process regulation of biological process regulation of cell cycle process biological regulation chromosome organization sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition organelle organization mitotic cell cycle process regulation of sister chromatid segregation nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle cellular process metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition ribonucleoprotein complex biogenesis positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process positive regulation of metabolic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process RNA processing rRNA metabolic process positive regulation of cellular process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of rRNA processing macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process ribosomal small subunit biogenesis maturation of SSU-rRNA establishment of organelle localization regulation of localization cellular localization nucleocytoplasmic transport transport positive regulation of nucleocytoplasmic transport positive regulation of ribosomal small subunit export from nucleus nuclear transport localization positive regulation of ribosomal subunit export from nucleus intercellular transport ribosomal small subunit export from nucleus organelle localization establishment of localization in cell positive regulation of intracellular transport nuclear export ribosome localization positive regulation of ribonucleoprotein complex localization ribonucleoprotein complex localization regulation of intracellular transport regulation of ribosomal small subunit export from nucleus regulation of ribonucleoprotein complex localization regulation of transport ribosomal subunit export from nucleus intracellular transport regulation of ribosomal subunit export from nucleus regulation of nucleocytoplasmic transport establishment of localization positive regulation of transport regulation of cellular localization protein phosphorylation protein autophosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process	preribosome protein-containing complex ribonucleoprotein complex preribosome, small subunit precursor cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle preribosome protein-containing complex ribonucleoprotein complex preribosome, small subunit precursor 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth G]	IPR018935	RIO kinase, conserved site	Conserved Site
A, B [auth G]	IPR030484	Serine/threonine-protein kinase Rio2	Domain
A, B [auth G]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B [auth G]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B [auth G]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B [auth G]	IPR015285	RIO2 kinase winged helix domain, N-terminal	Domain
A, B [auth G]	IPR018934	RIO-type domain	Domain
A, B [auth G]	IPR000687	RIO kinase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth G]	: Q9BVS4	Conventional (Clear Cell) Renal Cell Carcinoma ovarian cancer lung cancer osteosarcoma

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

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.