7B5M

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth C]SCOP2B SuperfamilyCullin repeat-like 8003460 3000059 SCOP2B (2022-06-29)
A [auth C]SCOP2B SuperfamilyWinged helix DNA-binding domain 8003455 3000034 SCOP2B (2022-06-29)
B [auth H]SCOP2B SuperfamilyRING/U-box like 8041693 3000160 SCOP2B (2022-06-29)
C [auth T]SCOP2B SuperfamilyF-box domain 8038678 3000567 SCOP2B (2022-06-29)
C [auth T]SCOP2B SuperfamilyRNI-like 8037339 3000990 SCOP2B (2022-06-29)
D [auth K]SCOP2B SuperfamilyCell cycle regulatory proteins 8037340 3000311 SCOP2B (2022-06-29)
E [auth S]SCOP2B SuperfamilyPOZ domain 8035033 3000894 SCOP2B (2022-06-29)
E [auth S]SCOP2B SuperfamilySkp1 dimerisation domain-like 8038683 3000564 SCOP2B (2022-06-29)
F [auth U]SCOP2B SuperfamilyUbiquitin-like 8043829 3000157 SCOP2B (2022-06-29)
G [auth R]SCOP2B SuperfamilyRING/U-box like 8040866 3000160 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth C]Cullin_4the7b5mC4 A: alpha arraysX: HTHH: HTHT: wingedF: Cullin_4thECOD (1.6)
A [auth C]Cullin_1ste7b5mC1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: Cullin_1stECOD (1.6)
A [auth C]Cullin_2nde7b5mC3 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: Cullin_2ndECOD (1.6)
A [auth C]Cullin_3rde7b5mC2 A: a+b duplicates or obligate multimersX: a+b domain in cullin-like proteins (From Topology)H: a+b domain in cullin-like proteins (From Topology)T: a+b domain in cullin-like proteinsF: Cullin_3rdECOD (1.6)
B [auth H]KOG1815_Ce7b5mH1 A: alpha bundlesX: N-cbl likeH: C-terminal domain of E3 ubiquitin-protein ligase ARIH1 (From Topology)T: C-terminal domain of E3 ubiquitin-protein ligase ARIH1F: KOG1815_CECOD (1.6)
B [auth H]IBR_2e7b5mH2 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: IBR domainF: IBR_2ECOD (1.6)
C [auth T]LRR_8_4e7b5mT2 A: beta duplicates or obligate multimersX: Single-stranded right-handed beta-helixH: Leucine-rich repeats (From Topology)T: Leucine-rich repeatsF: LRR_8_4ECOD (1.6)
C [auth T]F-box-likee7b5mT1 A: alpha arraysX: F-box domain (From Topology)H: F-box domain (From Topology)T: F-box domainF: F-box-likeECOD (1.6)
D [auth K]CKSe7b5mK1 A: a+b complex topologyX: Cell cycle regulatory proteins (From Topology)H: Cell cycle regulatory proteins (From Topology)T: Cell cycle regulatory proteinsF: CKSECOD (1.6)
E [auth S]Skp1_POZe7b5mS1 A: a+b two layersX: POZ domain (From Topology)H: POZ domain (From Topology)T: POZ domainF: Skp1_POZECOD (1.6)
F [auth U]ubiquitin_1e7b5mU1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_1ECOD (1.6)
G [auth R]zf-rbx1e7b5mR1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: zf-rbx1ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth C]PF00888Cullin family (Cullin)Cullin family- Repeat
B [auth H]PF22191IBR domain (IBR_1)IBR domainThis entry represents an IBR domain, related to Pfam:PF01485.Domain
C [auth T]PF12937F-box-like (F-box-like)F-box-likeThis is an F-box-like family.Domain
D [auth K]PF01111Cyclin-dependent kinase regulatory subunit (CKS)Cyclin-dependent kinase regulatory subunit- Domain
E [auth S]PF03931Skp1 family, tetramerisation domain (Skp1_POZ)Skp1 family, tetramerisation domain- Domain
E [auth S]PF01466Skp1 family, dimerisation domain (Skp1)Skp1 family, dimerisation domain- Domain
F [auth U]PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain
G [auth R]PF12678RING-H2 zinc finger domain (zf-rbx1)RING-H2 zinc finger domainThere are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell ...There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control [1].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth C]Cullin-1
B [auth H]E3 ubiquitin-protein ligase ARIH1
C [auth T]S-phase kinase-associated protein 2
D [auth K]Cyclin-dependent kinases regulatory subunit 1
E [auth S]S-phase kinase-associated protein 1
F [auth U]Polyubiquitin-C
G [auth R]E3 ubiquitin-protein ligase RBX1
H [auth P]Cyclin-dependent kinase inhibitor 1B

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth C]IPR045093CullinFamily
A [auth C]IPR019559Cullin protein, neddylation domainDomain
A [auth C]IPR016158Cullin homology domainDomain
A [auth C]IPR016157Cullin, conserved siteConserved Site
A [auth C]IPR001373Cullin, N-terminalDomain
A [auth C]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
A [auth C]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
A [auth C]IPR036317Cullin homology domain superfamilyHomologous Superfamily
A [auth C]IPR016159Cullin repeat-like-containing domain superfamilyHomologous Superfamily
B [auth H]IPR002867IBR domainDomain
B [auth H]IPR044066TRIAD supradomainDomain
B [auth H]IPR048962E3 ubiquitin-protein ligase ARIH1-like, UBA-like domainDomain
B [auth H]IPR018957Zinc finger, C3HC4 RING-typeDomain
B [auth H]IPR045840Ariadne domainDomain
B [auth H]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
B [auth H]IPR031127E3 ubiquitin ligase RBR familyFamily
B [auth H]IPR001841Zinc finger, RING-typeDomain
C [auth T]IPR036047F-box-like domain superfamilyHomologous Superfamily
C [auth T]IPR001810F-box domainDomain
C [auth T]IPR032675Leucine-rich repeat domain superfamilyHomologous Superfamily
C [auth T]IPR006553Leucine-rich repeat, cysteine-containing subtypeRepeat
D [auth K]IPR036858Cyclin-dependent kinase, regulatory subunit superfamilyHomologous Superfamily
D [auth K]IPR000789Cyclin-dependent kinase, regulatory subunitFamily
E [auth S]IPR016073SKP1 component, POZ domainDomain
E [auth S]IPR001232S-phase kinase-associated protein 1-likeFamily
E [auth S]IPR036296SKP1-like, dimerisation domain superfamilyHomologous Superfamily
E [auth S]IPR016072SKP1 component, dimerisationDomain
E [auth S]IPR011333SKP1/BTB/POZ domain superfamilyHomologous Superfamily
E [auth S]IPR016897S-phase kinase-associated protein 1Family
F [auth U]IPR019954Ubiquitin conserved siteConserved Site
F [auth U]IPR000626Ubiquitin-like domainDomain
F [auth U]IPR019956Ubiquitin domainDomain
F [auth U]IPR050158Ubiquitin and ubiquitin-likeFamily
F [auth U]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
G [auth R]IPR051031RING-box E3 Ubiquitin LigaseFamily
G [auth R]IPR024766Zinc finger, RING-H2-typeDomain
G [auth R]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
G [auth R]IPR001841Zinc finger, RING-typeDomain
H [auth P]IPR003175Cyclin-dependent kinase inhibitor domainDomain
H [auth P]IPR044898Cyclin-dependent kinase inhibitor domain superfamilyHomologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A [auth C]PharosQ13616
B [auth H]PharosQ9Y4X5
C [auth T]PharosQ13309
D [auth K]PharosP61024
E [auth S]PharosP63208
F [auth U]PharosP0CG48
G [auth R]PharosP62877
H [auth P]PharosP46527

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
H [auth P]DHA Parent Component: SER

RESIDAA0181

PSI-MOD :  dehydroalanine (Ser) MOD:00189 , dehydroalanine (Cys) MOD:00793 , dehydroalanine (Tyr) MOD:00824 , dehydroalanine MOD:01168 , dehydroalanine (Sec) MOD:01954
H [auth P]TPO Parent Component: THR

RESIDAA0181 , AA0038

PSI-MOD :  dehydroalanine (Ser) MOD:00189 , dehydroalanine (Cys) MOD:00793 , dehydroalanine (Tyr) MOD:00824 , dehydroalanine MOD:01168 , dehydroalanine (Sec) MOD:01954 , O-phospho-L-threonine MOD:00047