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- PDB-9sdy: Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2 -

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Basic information

Entry
Database: PDB / ID: 9sdy
TitleStructure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2
Components
  • Cullin-5
  • E3 ubiquitin-protein ligase ARIH2
  • L3A2-1
  • RING-box protein 2
KeywordsLIGASE / Complex
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 / cullin family protein binding / site of DNA damage / protein K63-linked ubiquitination / ubiquitin ligase complex / protein K48-linked ubiquitination / endoplasmic reticulum unfolded protein response / intrinsic apoptotic signaling pathway / post-translational protein modification / G1/S transition of mitotic cell cycle / Vif-mediated degradation of APOBEC3G / RING-type E3 ubiquitin transferase / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / calcium channel activity / Downregulation of ERBB2 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / copper ion binding / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain ...: / : / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / 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 / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ARIH2 / Cullin-5 / RING-box protein 2
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsSchulman, B.A. / Du, J.
Funding support Germany, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: L3A2-1
R: RING-box protein 2
C: Cullin-5
H: E3 ubiquitin-protein ligase ARIH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,98911
Polymers179,5314
Non-polymers4587
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein L3A2-1


Mass: 17854.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein RING-box protein 2 / Rbx2 / CKII beta-binding protein 1 / CKBBP1 / RING finger protein 7 / Regulator of cullins 2 / ...Rbx2 / CKII beta-binding protein 1 / CKBBP1 / RING finger protein 7 / Regulator of cullins 2 / Sensitive to apoptosis gene protein


Mass: 12697.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF7, RBX2, ROC2, SAG / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9UBF6, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase
#3: Protein Cullin-5 / CUL-5 / Vasopressin-activated calcium-mobilizing receptor 1 / VACM-1


Mass: 91085.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL5, VACM1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q93034
#4: Protein E3 ubiquitin-protein ligase ARIH2 / ARI-2 / Protein ariadne-2 homolog / RING-type E3 ubiquitin transferase ARIH2 / Triad1 protein


Mass: 57893.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARIH2, ARI2, TRIAD1, HT005 / Production host: Escherichia coli (E. coli)
References: UniProt: O95376, RBR-type E3 ubiquitin transferase
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NEDD8-CUL5-RBX2-ARIH2-E2V / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 200 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191502 / Symmetry type: POINT
RefinementHighest resolution: 3.06 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039295
ELECTRON MICROSCOPYf_angle_d0.55812595
ELECTRON MICROSCOPYf_dihedral_angle_d4.1231253
ELECTRON MICROSCOPYf_chiral_restr0.0411426
ELECTRON MICROSCOPYf_plane_restr0.0041616

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