2P63 | pdb_00002p63

Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CDC4_D	e2p63A1	A: a/b three-layered sandwiches	X: Kringle-like	H: Kringle-like	T: Kringle-like	F: CDC4_D	ECOD (v294.1)
B	CDC4_D	e2p63B1	A: a/b three-layered sandwiches	X: Kringle-like	H: Kringle-like	T: Kringle-like	F: CDC4_D	ECOD (v294.1)
C	CHS5_N	e2p63C1	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: CHS5_N	ECOD (v294.1)
D		e2p63D1	A: a/b three-layered sandwiches	X: Tautomerase/MIF-like	H: Tautomerase/MIF	T: Tautomerase/MIF	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.10.30.20	Special	Helix non-globular	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)
B	6.10.30.20	Special	Helix non-globular	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)
C	6.10.30.20	Special	Helix non-globular	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)
D	6.10.30.20	Special	Helix non-globular	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF16856	Cell division control protein 4 dimerisation domain (CDC4_D)	Cell division control protein 4 dimerisation domain	This is the dimerisation domain (D domain) of fungal cell division control protein 4 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cell division control protein 4	phosphoprotein binding protein binding binding phosphoserine residue binding protein phosphorylated amino acid binding RNA binding U3 snoRNA binding snoRNA binding nucleic acid binding ubiquitin binding ubiquitin-like protein binding	ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of SSU-rRNA cellular component organization or biogenesis RNA processing rRNA metabolic process endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of SSU-rRNA cellular component organization or biogenesis RNA processing rRNA metabolic process endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process ribosomal small subunit biogenesis nucleic acid metabolic process biosynthetic process cellular process metabolic process macromolecule metabolic process endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cell division sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process sexual reproduction reproductive process meiotic cell cycle cell cycle G2/M phase transition G2/M transition of mitotic cell cycle rRNA 5'-end processing endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) RNA 5'-end processing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membraneless organelle cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex nuclear SCF ubiquitin ligase complex nuclear protein-containing complex nuclear ubiquitin ligase complex 90S preribosome preribosome ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR019775	WD40 repeat, conserved site	Conserved Site
A, B, C, D	IPR001810	F-box domain	Domain
A, B, C, D	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
A, B, C, D	IPR031740	Cell division control protein 4, dimerisation domain	Domain
A, B, C, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR036047	F-box-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR001680	WD40 repeat	Repeat

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.