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- EMDB-54793: Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2~L3A2-1~Ub -

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Basic information

Entry
Database: EMDB / ID: EMD-54793
TitleStructure of Neddylated CUL5 C-terminal region-RBX2-ARIH2~L3A2-1~Ub
Map data
Sample
  • Complex: NEDD8-CUL5-RBX2-ARIH2~E2V~Ub
    • Protein or peptide: NEDD8
    • Protein or peptide: RING-box protein 2
    • Protein or peptide: Ubiquitin
    • Protein or peptide: L3A2-1
    • Protein or peptide: Cullin-5
    • Protein or peptide: E3 ubiquitin-protein ligase ARIH2
  • Ligand: ZINC ION
  • Ligand: 5-azanylpentan-2-one
KeywordsComplex / Ligase
Function / homology
Function and homology information


developmental cell growth / RBR-type E3 ubiquitin transferase / ERBB2 signaling pathway / reelin-mediated signaling pathway / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / regulation of neuron migration / protein K11-linked ubiquitination / protein neddylation / ubiquitin conjugating enzyme binding ...developmental cell growth / RBR-type E3 ubiquitin transferase / ERBB2 signaling pathway / reelin-mediated signaling pathway / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / regulation of neuron migration / protein K11-linked ubiquitination / protein neddylation / ubiquitin conjugating enzyme binding / NEDD8 ligase activity / response to redox state / : / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / hematopoietic stem cell proliferation / ubiquitin ligase complex scaffold activity / TGF-beta receptor signaling activates SMADs / regulation of proteolysis / cullin family protein binding / site of DNA damage / regulation of postsynapse assembly / protein K63-linked ubiquitination / anatomical structure morphogenesis / ubiquitin ligase complex / protein K48-linked ubiquitination / endoplasmic reticulum unfolded protein response / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / intrinsic apoptotic signaling pathway / post-translational protein modification / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / VLDLR internalisation and degradation / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / AUF1 (hnRNP D0) binds and destabilizes mRNA
Similarity search - Function
: / : / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / Nedd8-like ubiquitin / IBR domain / IBR domain / In Between Ring fingers ...: / : / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / Nedd8-like ubiquitin / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ARIH2 / Polyubiquitin-C / Ubiquitin-like protein NEDD8 / Cullin-5 / RING-box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsSchulman BA / Du J
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU3196/1-1 Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: E2 variants for probing E3 ubiquitin ligase activities.
Authors: Jiale Du / Gisele A Andree / Daniel Horn-Ghetko / Luca Stier / Jaspal Singh / Sebastian Kostrhon / Leo Kiss / Matthias Mann / Sachdev S Sidhu / Brenda A Schulman /
Abstract: E3 ligases partner with E2 enzymes to regulate vast eukaryotic biology. The hierarchical nature of these pairings, with >600 E3s and ~40 E2s in humans, necessitates that E2s cofunction with numerous ...E3 ligases partner with E2 enzymes to regulate vast eukaryotic biology. The hierarchical nature of these pairings, with >600 E3s and ~40 E2s in humans, necessitates that E2s cofunction with numerous different E3s. Here, focusing on E3s in the RING-between-RING (RBR) family and their partner UBE2L3 and UBE2D-family E2s, we report an approach to interrogate selected pathways. We screened phage-displayed libraries of structure-based E2 variants (E2Vs) to discover enzymes with enhanced affinity and specificity toward half of all RBR E3 ligases (ARIH1, ARIH2, ANKIB1, CUL9, HOIL1, HOIP, and RNF14). Collectively, these E2Vs allowed distinguishing actions of different cofunctioning E3s, obtaining high-resolution cryogenic Electron Microscopy (cryo-EM) structures of an RBR E3 in the context of a substrate-bound multiprotein complex, and profiling an endogenous RBR E3 response to an extracellular stimulus. Overall, we anticipate that E2V technology will be a generalizable tool to enable in-depth mechanistic and structural analysis of E3 ligase functions, and mapping their activity states and protein partners in cellular signaling cascades.
History
DepositionAug 15, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54793.png

Downloads & links

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Map

FileDownload / File: emd_54793.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 432 pix.
= 367.718 Å		0.85 Å/pix.
x 432 pix.
= 367.718 Å		0.85 Å/pix.
x 432 pix.
= 367.718 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.18384376 - 0.6079242
Average (Standard dev.)0.0013895155 (±0.010349373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 367.71838 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54793_msk_1.map
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Additional map: #3

Fileemd_54793_additional_1.map
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Additional map: #2

Fileemd_54793_additional_2.map
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Additional map: #1

Fileemd_54793_additional_3.map
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Sample components

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Entire : NEDD8-CUL5-RBX2-ARIH2~E2V~Ub

EntireName: NEDD8-CUL5-RBX2-ARIH2~E2V~Ub
Components
  • Complex: NEDD8-CUL5-RBX2-ARIH2~E2V~Ub
    • Protein or peptide: NEDD8
    • Protein or peptide: RING-box protein 2
    • Protein or peptide: Ubiquitin
    • Protein or peptide: L3A2-1
    • Protein or peptide: Cullin-5
    • Protein or peptide: E3 ubiquitin-protein ligase ARIH2
  • Ligand: ZINC ION
  • Ligand: 5-azanylpentan-2-one

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Supramolecule #1: NEDD8-CUL5-RBX2-ARIH2~E2V~Ub

SupramoleculeName: NEDD8-CUL5-RBX2-ARIH2~E2V~Ub / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 kDa/nm

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Macromolecule #1: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.086562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGGGGLR Q

UniProtKB: Ubiquitin-like protein NEDD8

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Macromolecule #2: RING-box protein 2

MacromoleculeName: RING-box protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.697436 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MADVEDGEET CALASHSGSS GSKSGGDKMF SLKKWNAVAM WSWDVECDTC AICRVQVMDA CLRCQAENKQ EDCVVVWGEC NHSFHNCCM SLWVKQNNRC PLCQQDWVVQ RIGK

UniProtKB: RING-box protein 2

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Macromolecule #3: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.519778 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRG

UniProtKB: Polyubiquitin-C

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Macromolecule #4: L3A2-1

MacromoleculeName: L3A2-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.998607 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSMVAASSRL MKELEEIRKA GMKNFRNIQV DEANLLTWQG LIVPDNPPYD KGAFRIEINF PAEYPFKPPK ITFKTKIYHP NIDEKGQVC LPVISAENWK PATKTDQVIQ SLIALVNDPQ PEHPLRADLA EEYSKDRKKF AKNAEEFTKK YGEKRPVD

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Macromolecule #5: Cullin-5

MacromoleculeName: Cullin-5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.085297 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MATSNLLKNK GSLQFEDKWD FMRPIVLKLL RQESVTKQQW FDLFSDVHAV CLWDDKGPAK IHQALKEDIL EFIKQAQARV LSHQDDTAL LKAYIVEWRK FFTQCDILPK PFCQLEITLM GKQGSNKKSN VEDSIVRKLM LDTWNESIFS NIKNRLQDSA M KLVHAERL ...String:
MATSNLLKNK GSLQFEDKWD FMRPIVLKLL RQESVTKQQW FDLFSDVHAV CLWDDKGPAK IHQALKEDIL EFIKQAQARV LSHQDDTAL LKAYIVEWRK FFTQCDILPK PFCQLEITLM GKQGSNKKSN VEDSIVRKLM LDTWNESIFS NIKNRLQDSA M KLVHAERL GEAFDSQLVI GVRESYVNLC SNPEDKLQIY RDNFEKAYLD STERFYRTQA PSYLQQNGVQ NYMKYADAKL KE EEKRALR YLETRRECNS VEALMECCVN ALVTSFKETI LAECQGMIKR NETEKLHLMF SLMDKVPNGI EPMLKDLEEH IIS AGLADM VAAAETITTD SEKYVEQLLT LFNRFSKLVK EAFQDDPRFL TARDKAYKAV VNDATIFKLE LPLKQKGVGL KTQP ESKCP ELLANYCDML LRKTPLSKKL TSEEIEAKLK EVLLVLKYVQ NKDVFMRYHK AHLTRRLILD ISADSEIEEN MVEWL REVG MPADYVNKLA RMFQDIKVSE DLNQAFKEMH KNNKLALPAD SVNIKILNAG AWSRSSEKVF VSLPTELEDL IPEVEE FYK KNHSGRKLHW HHLMSNGIIT FKNEVGQYDL EVTTFQLAVL FAWNQRPREK ISFENLKLAT ELPDAELRRT LWSLVAF PK LKRQVLLYEP QVNSPKDFTE GTLFSVNQEF SLIKNAKVQK RGKINLIGRL QLTTERMREE ENEGIVQLRI LRTQEAII Q IMKMRKKISN AQLQTELVEI LKNMFLPQKK MIKEQIEWLI EHKYIRRDES DINTFIYMA

UniProtKB: Cullin-5

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Macromolecule #6: E3 ubiquitin-protein ligase ARIH2

MacromoleculeName: E3 ubiquitin-protein ligase ARIH2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: RBR-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.893844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVDMNSQGS DSNEEDYDPN CEEEEEEEED DPGDIEDYYV GVASDVEQQG ADAFDPEEYQ FTCLTYKESE GALNEHMTSL ASVLKVSHS VAKLILVNFH WQVSEILDRY KSNSAQLLVE ARVQPNPSKH VPTSHPPHHC AVCMQFVRKE NLLSLACQHQ F CRSCWEQH ...String:
MSVDMNSQGS DSNEEDYDPN CEEEEEEEED DPGDIEDYYV GVASDVEQQG ADAFDPEEYQ FTCLTYKESE GALNEHMTSL ASVLKVSHS VAKLILVNFH WQVSEILDRY KSNSAQLLVE ARVQPNPSKH VPTSHPPHHC AVCMQFVRKE NLLSLACQHQ F CRSCWEQH CSVLVKDGVG VGVSCMAQDC PLRTPEDFVF PLLPNEELRE KYRRYLFRDY VESHYQLQLC PGADCPMVIR VQ EPRARRV QCNRCNEVFC FKCRQMYHAP TDCATIRKWL TKCADDSETA NYISAHTKDC PKCNICIEKN GGCNHMQCSK CKH DFCWMC LGDWKTHGSE YYECSRYKEN PDIVNQSQQA QAREALKKYL FYFERWENHN KSLQLEAQTY QRIHEKIQER VMNN LGTWI DWQYLQNAAK LLAKCRYTLQ YTYPYAYYME SGPRKKLFEY QQAQLEAEIE NLSWKVERAD SYDRGDLENQ MHIAE QRRR TLLKDFHDT

UniProtKB: E3 ubiquitin-protein ligase ARIH2

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: 5-azanylpentan-2-one

MacromoleculeName: 5-azanylpentan-2-one / type: ligand / ID: 8 / Number of copies: 1 / Formula: SY8
Molecular weightTheoretical: 101.147 Da
Chemical component information

ChemComp-SY8:
5-azanylpentan-2-one

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8oni

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 200442
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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