Table 1 Observed protein–protein interactions with RBR E3 ubiquitin ligases

Detection methods: 2H, yeast or mammalian-two hybrid; AUbA, autoubiquitination assay; CE, co-elution during chromatography purification; FRET, FRET in vivo; IF, immunofluorescence; IP, immunoprecipitation; ITC, isothermal calorimetry; LCMS, liquid chromatographyMS/MS; NMR, nuclear magnetic resonance; PD, pulldown using GST, His or MBP tag; Phos, in vitro phosphorylation; SPR, surface plasmon resonance; UbA, ubiquitination assay; UbSu, ubiquitin suicide inhibitor; X-ray, X-ray crystallography.

RBR E3 ligaseInteracting proteinDetection method(s)RBR-interaction siteReference(s)
ParkinUbcH7 (UBE2L3)IP, 2H, AUbA, UbA, SPRRING1[24,25,29,46,47,51,60,78,80,82,9194,127,132,137144]
UbcH5c (UBE2D3)/Ubc7 (UBE2G1)/UbcH6 (UBE2E1)IP, UbA[93,140,144,145]
UbcH8 (UBE2L6)/UbcH13 (UBE2N)IP, PD, UbARcat[24,26,47,61]
Ubiquitin-conjugating enzyme Variant 1a (Uev1a)PDRING1[61]
14-3-3ηIP, PD, UbARING0[143]
20S proteasome subunit α4 (PSMA7/XAPC7, subunit α type7)2H, IPBRcat–Rcat[83]
26S proteasome non-ATPase reg. subunit4 (Rpn10/S5a)UbA, PD, NMRUbl[30,7982]
α-Synuclein-interacting protein (Synphylin-1, Sph1)IP, UbA, PDRcat[94,141,143,145,146]
All 1-fused gene from chromosome 6 (Afadin/AF-6)IP, PDRcat[147]
Aminoacyl tRNA synthase complex coactivator (p38/JTV-1/AIMP2)IP, PDUbl, RING1[82,91,94,146,148150]
Apoptosis regulator Bcl-2IP, PD[151]
Bcl-2-associated athanogene 5 (BAG5)IP, PD, UbA[152,153]
Calcium/calmodulin dependent serine kinase (CASK/Lin2)IP, PD, UbARcat[92]
Carboxy terminus of Hsp70-interacting protein (CHIP)IP, PD[63]
Casein kinase 1 (CK1)IP, PD, PhosSer101, Ser378[95,98]
Catenin β-1 (β-catenin)PD[154]
Chondroitin-polymerizing factor (ChPF/Klokin1)IP, 2H[155]
CulIP, PD[132]
Cdk5IP, PDSer131[94,95]
Cyclin EIP, PD, UbA[132,142,156]
DJ-1 peptidaseIP, PD, UbA[47,145,157,158]
Dopamine transporter (DAT)IP, PD[64]
E3 SUMO-protein ligase RanBP2IP, 2H, UbA[78]
Endophillin-A1PD, UbA, NMRUbl[111]
Eps15PD, UbA, NMR, ITCUbl[30,31]
F-box/WD repeat-containing protein 7 (FBX30/SEL-10)IP, PDΔUbl[132]
Heat-shock 70 kDa protein (Hsp70/chaperone protein DnaK)IPΔUbl[63,82,127]
HDAC6IP, PDRING0, RING1, Rcat[70,71]
Leu-rich PPR motif-containing protein (LRPPRC, LRP130)IP[59]
Leu-rich repeat kinase 2 (LRRK2)IPRcat[90]
LIM kinase-1 (LIMK1)IP, UbABRcat–Rcat[91]
Machado–Joseph disease protein 1 (Ataxin-3)IP, UbA, PD, NMRUbl, BRcat–Rcat[110,127,139,140]
Mitochondrial Rho GTPase (Miro)IP[159,160]
Mitofusin-1 & 2 (MFN1, MFN2)IP, UbA[49,5157]
Mortalin (HSPA9, GRP75, PBP74)IP[161]
Neuronal DnaJ/Hsp40 chaperone HSJ1a (DNAJB2a)IP[162]
O-glycosylated α-synuclein (αSp22)IP, UbA[6062]
Parkin-associated endothelin receptor (Pael-R)IP, UbA[46,63]
Parkin co-regulated gene protein (PACRG/Glup)IP[163]
Parkin-interacting substrate (PARIS/ZNF476)IP, PD, UbARING1, Rcat[144]
Prolierating cell nuclear antigen (PCNA)IPRING1[68,69]
Protein interacting with C kinase 1 (PICK1/PRKCA BP)IP, PD, UbARcat[93]
Protein kinase A (PKA)PhosSer101, Ser131, Ser236, Ser378[98]
Protein kinase C (PKC)PhosSer296, Ser378[98]
PINK1IP, UbA, Phos, PD, LCMSSer65, Thr175[49,99102,145,164168]
RNF41/NRDP1/FLRFIP, 2H, PD, UbAUbl[150,169]
Septin4 (ARTS/CDCrel-2)/Septin5 (CDCrel-1/PNUTL1)IP, 2H, PDRBR[26,82,83,138,170]
Small ubiquitin-related modifer-1 (SUMO-1)IP, PD[77]
Synaptotagmin XI (Syt11)2H, IP, UbARING1[171]
TDP-43IP, PD[71]
Transcription factor single-minded 2 (SIM2)IPBRcat–Rcat[72]
TOMM70AIP, PD[58,59]
Tubulin (α, β & γ)IP, PD, CERING0, RING1, Rcat[82,172174]
Tyrosine protein kinase ABL1 (c-Abl)IP, PDTyr143[96,97]
HHARI (Ariadne 1)UbcH7 (UBE2L3)IP, 2H, IF, CE, ITC, PD, UbARING1[27,29,37,42,114,175]
UbcH8 (UBE2L6)IPRcat[27]
α-SynucleinIF[176]
α-Synuclein interacting protein (Synphilin-1, Sph1)IF[176]
Cul-1,2,3,4A (NEDD8-dependent)IP, UbSuAcidic/Gly[37]
Transcription factor single-minded (SIM2)IP[72]
Translation initiation factor 4F homologous protein (4EHP)IP, 2HRING1[76]
TRIAD1 (Ariadne-2)UbcH7 (UBE2L3)IP, 2H, PD, PD, UbARING1[37,177179]
UbcH6 (UBE2E1/UbcH8 (UBE2L6)/UbcH13 (UBE2N)IP, 2H, PDRcat[177179]
Cul-5 (NEDD8-dependent)IP, UbA[37]
Growth factor independence 1 & 1B (Gfi1, Gfi1B)IP, 2H, PDRcat[180]
MDM2UbA[84]
Nuclear Inhibitor of NF-κB β (IκBβ)IP[181]
p53IP, PD[182,183]
Promyelocytic leukaemia-retinoic acid receptor α (PML-RARα)IP, IF[179]
Parc (CUL9)UbcH7 (UBE2L3)UbA[131]
Cul-7IP[88,184]
NEDD8IP, LCMSCullin at Lys1881[88,89]
p53IP, PD, IF, CE, NMRCPH[41,88,131,185]
Ring box protein-1 (Rbx1)IP[88]
ARA54 (RNF14, HRIHFB2038, HFB30 and TRIAD2)UbcH6 (UBE2E1)/UbcH8 (UBE2L6)/UbcH9 (UBE2E3)2H, AUbARING1[186]
Androgen receptorIP, 2H, PD, SPR, FRET, X-rayC-term FXXL(F/Y)[73,74,187194]
Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1)2H, M2H, PD[195]
p300/CBP-associated factor2H[188]
T-cell factors 1 & 4 (TCF1, TCF4)IP, PD[196]
TRIAD3 (RNF216, ZIN)UbcH7 (UBE2L3)/UbcH8 (UBE2L6)IP[197]
Killer cell Ig-like receptor (KIR) 2DL4IP, 2HRBR[198]
Receptor interacting serine/threonine-protein kinase-1 (RIP1)IP[103]
TNF receptor-associated factor 3 (TRAF3)IPN-term PXQX(T/S)[199]
Toll/interleukin-1 receptor adaptor protein (TIRAP)IP[103]
Toll-like receptors 3,4,5, and 9 (TLR3,4,5,9)2H[197]
Virion infectivity factor (Vif) of HIV-1IP, PD[200]
HOIP (PAUL, RNF31)HOIL-1IP, PD, CE, UbA, SPR, X-ray, NMRUBA (via HOIL-1 Ubl)[32,38,4345,134,201203]
Sharpin (Sipl1)IP, CE, UbANZF2[38,43,45,133,134,202205]
UbcH7 (UBE2L3)UbARING1–BRcat[38,44,45,201,206]
UbcH5A (UBE2D1)/UbcH5B (UBE2D2)/UbcH5C (UBE2D3)UbARING1–BRcat[39,4345,65,85,105,134,201]
E2-25K (UBE2K)UbA[201]
NEMOIP, PD, UbA[39,65,67,133,134,205207]
B-cell surface antigen CD40 (CD40)IP[207]
Muscle-Specific receptor tyrosine Kinase (MuSK)2H[104]
Nucleotide-binding oligomerization domain protein 2 (NOD2)IP[208,209]
OTU domain deubiquitinase with linear link specificity (Gumby)IP[87]
Polyubiquitin chains (Lys63>linear>Lys48)IP, PD, ITCNZF1[38,66,210]
Tumour necrosis factor receptor 1 signalling complex (TNF-RSC)IP[66,85,211]
HOIL-1cIAP1/2IP[66]
Nucleotide-binding oligomerization domain protein 2 (NOD2)IP[208,209]
Polyubiquitin chains (linear>Lys63)PD, SPR, X-ray, ITCUbl, NZF[38,39,66,210]
Protein kinase C (PKC)2H, UbAUbl[105]
Retinoic acid-inducible gene 1 protein (RIG-1)PDNZF[85]
Suppressor of cytokine signalling 6 (SOCS-6)IP, 2HUbl[212]
Tumour necrosis factor α-induced protein 3 (A20)IP[211]
Tumour receptor-associated factor 2 (TRAF2)IP[66]
RNF144AUbcH7 (UBE2L3)2H[213]
RNF144B (p53RFP/IBRDC2/PIR2)UbcH7 (UBE2L3)/UbcH8 (UBE2L6)IPRBR[214]
Bcl-2 associated protein X (BAX)IP[215]
CDK-interacting protein 1 (p21WAF1)IP[216]
Leukaemic nucleophosmin protein (NPMc)IP[217]
p53, p63, p73IP[216,218220]
Dorfin (RNF19)UbcH7 (UBE2L3)/UbcH8 (UBE2L6)IPRBR[221]
α-Synuclein interacting protein (Synphillin-1, Sph1)IP, UbA[222]
Calcium-sensing receptorIP, 2HC-terminal extension[223]
Cu/Zn SOD1 (ALS mutants; G37R/H46R/G85R/G93A)IP, UbAC-terminal extension[224228]
Ubiquitinated-substrates (not defined)IPRBR and C-terminal extension[221]
Valosin-containing protein (p97/Cdc48 homologue)IP, IF, LCMS[223,226]
VimentinIF[221]