9KBD | pdb_00009kbd

Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
D [auth A]SCOP2B SuperfamilyWinged helix DNA-binding domain 8003455 3000034 SCOP2B (2022-06-29)
D [auth A]SCOP2B SuperfamilyCullin repeat-like 8003460 3000059 SCOP2B (2022-06-29)
D [auth A]SCOP2B SuperfamilyWinged helix DNA-binding domain 8003463 3000034 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyMPT63/MPB63-like 8086822 3002065 SCOP2B (2022-06-29)
A [auth B]SCOP2B SuperfamilySkp1 dimerisation domain-like 8038683 3000564 SCOP2B (2022-06-29)
A [auth B]SCOP2B SuperfamilyPOZ domain 8035033 3000894 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
D [auth A]PF00888Cullin alpha solenoid domain (Cullin)Cullin alpha solenoid domain- Repeat
D [auth A]PF10557Cullin protein neddylation domain (Cullin_Nedd8)Cullin protein neddylation domainThis 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
B [auth C]PF00646F-box domain (F-box)F-box domainThis domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; Pfam:PF00560 and Pfam:PF07 ...This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; Pfam:PF00560 and Pfam:PF07723) and the WD repeat (Pfam:PF00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression [1-2].
Domain
B [auth C]PF09346SMI1 / KNR4 family (SUKH-1) (SMI1_KNR4)SMI1 / KNR4 family (SUKH-1)Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation [1][2]. Genome contextual information showed that SMI1 are primary immunity proteins in bacterial toxin systems [3]. Domain
B [auth C]PF04379ApaG domain (DUF525)ApaG domain- Family
A [auth B]PF03931Skp1 family, tetramerisation domain (Skp1_POZ)Skp1 family, tetramerisation domainDomain
A [auth B]PF01466Skp1 family, dimerisation domain (Skp1)Skp1 family, dimerisation domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
D [auth A]Cullin-1
C [auth R]E3 ubiquitin-protein ligase RBX1
B [auth C]F-box only protein 3
A [auth B]S-phase kinase-associated protein 1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
D [auth A]IPR045093CullinFamily
D [auth A]IPR016158Cullin homology domainDomain
D [auth A]IPR016157Cullin, conserved siteConserved Site
D [auth A]IPR001373Cullin, N-terminalDomain
D [auth A]IPR019559Cullin, neddylation domainDomain
D [auth A]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
D [auth A]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
D [auth A]IPR036317Cullin homology domain superfamilyHomologous Superfamily
D [auth A]IPR016159Cullin repeat-like-containing domain superfamilyHomologous Superfamily
C [auth R]IPR051031RING-box E3 Ubiquitin LigaseFamily
C [auth R]IPR024766Zinc finger, RING-H2-typeDomain
C [auth R]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
C [auth R]IPR001841Zinc finger, RING-typeDomain
B [auth C]IPR036047F-box-like domain superfamilyHomologous Superfamily
B [auth C]IPR007474ApaG domainDomain
B [auth C]IPR001810F-box domainDomain
B [auth C]IPR052121F-box Protein Family Substrate Recognition ComponentsFamily
B [auth C]IPR018958Knr4/Smi1-like domainDomain
B [auth C]IPR037883Knr4/Smi1-like domain superfamilyHomologous Superfamily
B [auth C]IPR036767ApaG domain superfamilyHomologous Superfamily
A [auth B]IPR016073SKP1 component, POZ domainDomain
A [auth B]IPR001232S-phase kinase-associated protein 1-likeFamily
A [auth B]IPR036296SKP1-like, dimerisation domain superfamilyHomologous Superfamily
A [auth B]IPR016072SKP1 component, dimerisationDomain
A [auth B]IPR011333SKP1/BTB/POZ domain superfamilyHomologous Superfamily
A [auth B]IPR016897S-phase kinase-associated protein 1Family

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
D [auth A]PharosQ13616
C [auth R]PharosP62877
B [auth C]PharosQ9UK99
A [auth B]PharosP63208