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- EMDB-62356: cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb... -

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Basic information

Entry
Database: EMDB / ID: EMD-62356
Titlecryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (dimeric conformation)
Map data
Sample
  • Complex: Ufd2/Ufd4-Ub in complex with K29-linked diUb (dimeric conformation)
KeywordsE4 enzyme / Ub ligase / Ufd2 / Ubc4 / Branching / K48/29 / LYASE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.84 Å
AuthorsAi HS / Tong ZB / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2137005, 92253302, 22227810, 22407121, T2488301, 22277073 and 92253302 China
CitationJournal: Nat Chem Biol / Year: 2025
Title: Structural basis for E4 enzyme Ufd2-catalyzed K48/K29 branched ubiquitin chains.
Authors: Zebin Tong / Xiangwei Wu / Hongyi Cai / Shidian Wu / Tianyi Zhang / Zhiheng Deng / Ziyu Xu / Rujing Yuan / Huasong Ai / Lei Liu / Man Pan /
Abstract: E4 enzymes amplify and remodel ubiquitin chain signals beyond the conventional E1-E2-E3 cascade. The first identified E4 enzyme Ufd2 preferentially catalyzes K48/K29 branched ubiquitin chains, yet ...E4 enzymes amplify and remodel ubiquitin chain signals beyond the conventional E1-E2-E3 cascade. The first identified E4 enzyme Ufd2 preferentially catalyzes K48/K29 branched ubiquitin chains, yet the structural mechanism remains unknown. Here, we combined chemical biology and cryo-electron microscopy to visualize stable intermediates in Ufd2 loading ubiquitin at K48 of proximal ubiquitin on K29-linked di- and triubiquitin. Our data reveal that the core region of Ufd2 functions as an unprecedented K29 diubiquitin binding domain, interacting extensively with proximal and distal ubiquitin, which orients the K48 site of proximal ubiquitin toward the active site of Ubc4, facilitating K48/K29 branched ubiquitin chain formation. We also identified a unique dimeric conformation where dimerized Ufd2 and Ubc4 stabilize each other's distal ubiquitin during branching on K29 triubiquitin. Our findings provide mechanistic insights into the assembly of K48/K29 branched ubiquitin chains by the E4 enzyme Ufd2 and highlight the spatial cooperation among multiple pairs of ubiquitin-related enzymes on longer ubiquitin chains.
History
DepositionNov 11, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62356.png

Downloads & links

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Map

FileDownload / File: emd_62356.map.gz / Format: CCP4 / Size: 244.1 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.)
1.1 Å/pix.
x 400 pix.
= 439.16 Å		1.1 Å/pix.
x 400 pix.
= 439.16 Å		1.1 Å/pix.
x 400 pix.
= 439.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.007436952 - 0.027892724
Average (Standard dev.)0.000024930821 (±0.00096352655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 439.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62356_msk_1.map
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Additional map: #1

Fileemd_62356_additional_1.map
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Half map: #1

Fileemd_62356_half_map_1.map
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Half map: #2

Fileemd_62356_half_map_2.map
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Sample components

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Entire : Ufd2/Ufd4-Ub in complex with K29-linked diUb (dimeric conformation)

EntireName: Ufd2/Ufd4-Ub in complex with K29-linked diUb (dimeric conformation)
Components
  • Complex: Ufd2/Ufd4-Ub in complex with K29-linked diUb (dimeric conformation)

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Supramolecule #1: Ufd2/Ufd4-Ub in complex with K29-linked diUb (dimeric conformation)

SupramoleculeName: Ufd2/Ufd4-Ub in complex with K29-linked diUb (dimeric conformation)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48544
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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