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- EMDB-54893: Focus refined map of Neddylated CUL5-ARIH2-L3A2-1 bound to ASB9-E... -

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Basic information

Entry
Database: EMDB / ID: EMD-54893
TitleFocus refined map of Neddylated CUL5-ARIH2-L3A2-1 bound to ASB9-EloB/C-CKB, focus refined on ARIH2-L3A2-1
Map data
Sample
  • Complex: NEDD8-CUL5-RBX2-ARIH2-E2V
KeywordsComplex / Ligase
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 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 25, 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_54893.png

Downloads & links

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Map

FileDownload / File: emd_54893.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.51593673 - 0.74711055
Average (Standard dev.)-0.0004924625 (±0.008522773)
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_54893_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #1

Fileemd_54893_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_54893_half_map_2.map
Projections & Slices
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Sample components

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Entire : NEDD8-CUL5-RBX2-ARIH2-E2V

EntireName: NEDD8-CUL5-RBX2-ARIH2-E2V
Components
  • Complex: NEDD8-CUL5-RBX2-ARIH2-E2V

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

SupramoleculeName: NEDD8-CUL5-RBX2-ARIH2-E2V / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 kDa/nm

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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: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 191502
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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