Annotations: 1IUY

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1iuya_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	SCF ubiquitin ligase complex WHB domain	Cullin-3 homologue	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SCF complex WHB domain-like	8003467	4000322	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8057695	3000034	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)
A	Cullin_Nedd8	e1iuyA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Cullin_Nedd8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF10557	Cullin protein neddylation domain (Cullin_Nedd8)	Cullin protein neddylation domain	This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cu ...	This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	cullin-3 homologue	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding signaling receptor binding Notch binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding signaling receptor binding Notch binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding POZ domain binding protein domain specific binding identical protein binding cyclin binding	cellular response to stimulus response to organic substance catabolic process response to stimulus proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein organic substance metabolic process cellular response to stress modification-dependent macromolecule catabolic process proteolysis response to stress cellular response to stimulus response to organic substance catabolic process response to stimulus proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein organic substance metabolic process cellular response to stress modification-dependent macromolecule catabolic process proteolysis response to stress protein metabolic process cellular response to organic substance organonitrogen compound catabolic process organonitrogen compound metabolic process cellular response to topologically incorrect protein primary metabolic process proteasomal protein catabolic process protein catabolic process nuclear protein quality control by the ubiquitin-proteasome system cellular response to chemical stimulus modification-dependent protein catabolic process response to chemical response to topologically incorrect protein ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins organic substance catabolic process developmental process multicellular organism development multicellular organismal process embryonic cleavage anatomical structure development cell division embryo development gland development animal organ development liver development anatomical structure morphogenesis gland morphogenesis hepaticobiliary system development animal organ morphogenesis liver morphogenesis system development regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of type I interferon production cytokine production organic substance biosynthetic process negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process type I interferon production cellular metabolic process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production regulation of cytokinesis positive regulation of cell division regulation of cell cycle process positive regulation of biological process cytokinesis positive regulation of cell cycle regulation of cell division positive regulation of cytokinesis positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process protein destabilization regulation of protein stability regulation of biological quality anaphase-promoting complex-dependent catabolic process establishment of organelle localization cellular localization mitotic metaphase chromosome alignment mitotic cell cycle metaphase chromosome alignment cellular component organization localization chromosome localization organelle localization establishment of localization in cell mitotic sister chromatid segregation cellular component organization or biogenesis chromosome segregation mitotic nuclear division organelle fission chromosome organization sister chromatid segregation establishment of localization organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation establishment of chromosome localization vesicle budding from membrane transport vesicle targeting, to, from or within Golgi vesicle-mediated transport vesicle targeting vesicle organization cellular component biogenesis cellular component assembly protein-containing complex assembly vesicle coating vesicle targeting, rough ER to cis-Golgi membrane organization vesicle localization protein-containing complex organization establishment of vesicle localization intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport COPII-coated vesicle budding COPII vesicle coating Golgi vesicle transport regulation of cell cycle phase transition cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of mitotic cell cycle mitotic cell cycle phase transition protein autoubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal actomyosin structure organization actin cytoskeleton organization actin filament organization actin filament bundle organization contractile actin filament bundle assembly actin filament-based process actin filament bundle assembly stress fiber assembly supramolecular fiber organization cytoskeleton organization cell migration cell motility embryo development ending in birth or egg hatching chordate embryonic development in utero embryonic development fibroblast apoptotic process apoptotic process cell death programmed cell death protein polyubiquitination cell morphogenesis cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid protein K48-linked ubiquitination stem cell division regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process protein monoubiquitination positive regulation of organelle organization regulation of mitotic nuclear division positive regulation of mitotic nuclear division positive regulation of mitotic metaphase/anaphase transition mitotic sister chromatid separation positive regulation of nuclear division regulation of chromosome organization regulation of organelle organization regulation of chromosome separation regulation of chromosome segregation regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization regulation of mitotic sister chromatid separation positive regulation of cellular component organization regulation of mitotic metaphase/anaphase transition positive regulation of metaphase/anaphase transition of cell cycle chromosome separation regulation of sister chromatid segregation positive regulation of mitotic sister chromatid separation regulation of nuclear division metaphase/anaphase transition of mitotic cell cycle positive regulation of chromosome separation metaphase/anaphase transition of cell cycle regulation protein catabolic process at synapse regulation of catabolic process regulation protein catabolic process at postsynapse embryonic morphogenesis gastrulation integrin-mediated signaling pathway cell surface receptor signaling pathway signaling cell communication signal transduction regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of TORC1 signaling intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling regulation of TORC1 signaling TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication TORC1 signaling positive regulation of signaling small GTPase-mediated signal transduction negative regulation of Rho protein signal transduction negative regulation of signaling regulation of small GTPase mediated signal transduction negative regulation of intracellular signal transduction Rho protein signal transduction negative regulation of cell communication intracellular signaling cassette negative regulation of response to stimulus negative regulation of small GTPase mediated signal transduction regulation of Rho protein signal transduction negative regulation of signal transduction trophectodermal cell differentiation cellular developmental process blastocyst formation cell differentiation trophectodermal cellular morphogenesis anatomical structure formation involved in morphogenesis blastocyst development Wnt signaling pathway defense response inflammatory response cell projection organization	intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle intracellular non-membrane-bounded organelle spindle pole cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle polymeric cytoskeletal fiber spindle microtubule polar microtubule supramolecular fiber intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle intracellular non-membrane-bounded organelle spindle pole cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle polymeric cytoskeletal fiber spindle microtubule polar microtubule supramolecular fiber microtubule supramolecular polymer supramolecular complex membrane-bounded organelle cell projection cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection cytoplasm synapse cell junction glutamatergic synapse Golgi apparatus intracellular membrane-bounded organelle endomembrane system postsynapse centrosome microtubule organizing center cell periphery plasma membrane membrane mitotic spindle cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex Cul3-RING ubiquitin ligase complex intracellular protein-containing complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR045093	Cullin	Family
A	IPR019559	Cullin protein, neddylation domain	Domain
A	IPR016158	Cullin homology domain	Domain
A	IPR001373	Cullin, N-terminal	Domain
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A	IPR016157	Cullin, conserved site	Conserved Site
A	IPR036317	Cullin homology domain superfamily	Homologous Superfamily
A	IPR016159	Cullin repeat-like-containing domain superfamily	Homologous Superfamily

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.