7B5N

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth C]SCOP2B SuperfamilyWinged helix DNA-binding domain 8003455 3000034 SCOP2B (2022-06-29)
A [auth C]SCOP2B SuperfamilyWinged helix DNA-binding domain 8003463 3000034 SCOP2B (2022-06-29)
B [auth H]SCOP2B SuperfamilyRING/U-box like 8041693 3000160 SCOP2B (2022-06-29)
C [auth U]SCOP2B SuperfamilyUbiquitin-like 8043829 3000157 SCOP2B (2022-06-29)
D [auth N]SCOP2B SuperfamilyUbiquitin-like 8034470 3000157 SCOP2B (2022-06-29)
E [auth R]SCOP2B SuperfamilyRING/U-box like 8040866 3000160 SCOP2B (2022-06-29)
F [auth D]SCOP2B SuperfamilyUBC-like 8034823 3000570 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth C]Cullin_Nedd8e7b5nC3 A: alpha arraysX: HTHH: HTHT: wingedF: Cullin_Nedd8ECOD (1.6)
A [auth C]Cullin_4the7b5nC4 A: alpha arraysX: HTHH: HTHT: wingedF: Cullin_4thECOD (1.6)
A [auth C]Cullin_1ste7b5nC5 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: Cullin_1stECOD (1.6)
A [auth C]Cullin_2nde7b5nC2 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: Cullin_2ndECOD (1.6)
A [auth C]Cullin_3rde7b5nC1 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_Ne7b5nH2 A: alpha arraysX: RuvA-CH: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)T: RuvA-C, UBA, CRAL/TRIO-N, HBS1F: KOG1815_NECOD (1.6)
B [auth H]KOG1815_Ce7b5nH1 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]zf-C3HC4_4e7b5nH4 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: zf-C3HC4_4ECOD (1.6)
B [auth H]IBR_2e7b5nH5 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: IBR domainF: IBR_2ECOD (1.6)
B [auth H]IBRe7b5nH3 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: IBR domainF: IBRECOD (1.6)
C [auth U]ubiquitin_1e7b5nU1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_1ECOD (1.6)
D [auth N]ubiquitin_4e7b5nN1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_4ECOD (1.6)
E [auth R]zf-rbx1e7b5nR1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: zf-rbx1ECOD (1.6)
F [auth D]UQ_cone7b5nD1 A: a+b two layersX: UBC-likeH: UBC-like (From Topology)T: UBC-likeF: UQ_conECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth C]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 H]PF21235E3 ubiquitin-protein ligase ARIH1, UBA-like domain (ARI1_UBAl)E3 ubiquitin-protein ligase ARIH1, UBA-like domainThis entry represents the UBA-like (UBL) domain from the Human Homologue of Ariadne (HHARI) and its homologues, which are Ariadne subfamily E3 ubiquitin ligase proteins [1-4]. This domain binds to Ubiquitin and NEDD8 [3,4].Domain
B [auth H]PF00097Zinc finger, C3HC4 type (RING finger) (zf-C3HC4)Zinc finger, C3HC4 type (RING finger)The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [1]. Many protein ...The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [1]. Many proteins containing a RING finger play a key role in the ubiquitination pathway [2].
Domain
B [auth H]PF01485IBR domain, a half RING-finger domain (IBR)IBR domain, a half RING-finger domainThe IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (Pfam:PF00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain [2]. Proteins that contain two Ring fing ...The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (Pfam:PF00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain [2]. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription [3]. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease [3][4].
Domain
B [auth H]PF22191IBR domain (IBR_1)IBR domainThis entry represents an IBR domain, related to Pfam:PF01485.Domain
C [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
D [auth N]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
E [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
F [auth D]PF00179Ubiquitin-conjugating enzyme (UQ_con)Ubiquitin-conjugating enzymeProteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].
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 U]Polyubiquitin-C
D [auth N]NEDD8
E [auth R]E3 ubiquitin-protein ligase RBX1
F [auth D]Ubiquitin-conjugating enzyme E2 L3

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 U]IPR019954Ubiquitin conserved siteConserved Site
C [auth U]IPR000626Ubiquitin-like domainDomain
C [auth U]IPR019956Ubiquitin domainDomain
C [auth U]IPR050158Ubiquitin and ubiquitin-likeFamily
C [auth U]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
D [auth N]IPR019954Ubiquitin conserved siteConserved Site
D [auth N]IPR000626Ubiquitin-like domainDomain
D [auth N]IPR019956Ubiquitin domainDomain
D [auth N]IPR050158Ubiquitin and ubiquitin-likeFamily
D [auth N]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
D [auth N]IPR038738Nedd8-like ubiquitinDomain
E [auth R]IPR051031RING-box E3 Ubiquitin LigaseFamily
E [auth R]IPR024766Zinc finger, RING-H2-typeDomain
E [auth R]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
E [auth R]IPR001841Zinc finger, RING-typeDomain
F [auth D]IPR050113Ubiquitin-conjugating enzymeFamily
F [auth D]IPR016135Ubiquitin-conjugating enzyme/RWD-likeHomologous Superfamily
F [auth D]IPR000608Ubiquitin-conjugating enzyme E2Domain
F [auth D]IPR023313Ubiquitin-conjugating enzyme, active siteActive Site

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A [auth C]PharosQ13616
B [auth H]PharosQ9Y4X5
C [auth U]PharosP0CG48
D [auth N]PharosQ15843
E [auth R]PharosP62877
F [auth D]PharosP68036