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- EMDB-35931: cryo-EM structures of Ufd4 in complex with Ubc4-Ub -

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Basic information

Entry
Database: EMDB / ID: EMD-35931
Titlecryo-EM structures of Ufd4 in complex with Ubc4-Ub
Map dataUfd4 without ARM domain in complex with Ubc4 at a resolution of 3.52 Angstrom
Sample
  • Complex: Ufd4 in complex with Ubc4-Ub
    • Complex: Ufd4
      • Protein or peptide: Ubiquitin fusion degradation protein 4
    • Complex: Ubc4
      • Protein or peptide: Ubiquitin-conjugating enzyme E2 4
KeywordsUfd4 / Ubc4 / Ubc4-Ub / HECT-type E3 ligase / LIGASE
Function / homology
Function and homology information


proteasome regulatory particle binding / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein K29-linked ubiquitination / free ubiquitin chain polymerization / mitochondria-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase ...proteasome regulatory particle binding / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein K29-linked ubiquitination / free ubiquitin chain polymerization / mitochondria-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / Transferases; Acyltransferases; Aminoacyltransferases / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / rescue of stalled ribosome / ubiquitin binding / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / cellular response to heat / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase HECTD1/TRIP12-like / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme ...E3 ubiquitin-protein ligase HECTD1/TRIP12-like / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 4 / Ubiquitin fusion degradation protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsAi HS / Mao JX / Wu XW / Cai HY / Pan M / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810, 22277073, 92253302, China
CitationJournal: Nat Commun / Year: 2025
Title: Structural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination.
Authors: Xiangwei Wu / Huasong Ai / Junxiong Mao / Hongyi Cai / Lu-Jun Liang / Zebin Tong / Zhiheng Deng / Qingyun Zheng / Lei Liu / Man Pan /
Abstract: The K29/K48-linked ubiquitination generated by the cooperative catalysis of E3 ligase Ufd4 and Ubr1 is an enhanced protein degradation signal, in which Ufd4 is responsible for introducing K29-linked ...The K29/K48-linked ubiquitination generated by the cooperative catalysis of E3 ligase Ufd4 and Ubr1 is an enhanced protein degradation signal, in which Ufd4 is responsible for introducing K29-linked ubiquitination to K48-linked ubiquitin chains to augment polyubiquitination. How HECT-E3 ligase Ufd4 mediates the ubiquitination event remains unclear. Here, we biochemically determine that Ufd4 preferentially catalyses K29-linked ubiquitination on K48-linked ubiquitin chains to generate K29/K48-branched ubiquitin chains and capture structural snapshots of Ub transfer cascades for Ufd4-mediated ubiquitination. The N-terminal ARM region and HECT domain C-lobe of Ufd4 are identified and characterized as key structural elements that together recruit K48-linked diUb and orient Lys29 of its proximal Ub to the active cysteine of Ufd4 for K29-linked branched ubiquitination. These structures not only provide mechanistic insights into the architecture of the Ufd4 complex but also provide structural visualization of branched ubiquitin chain formation by a HECT-type E3 ligase.
History
DepositionApr 13, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35931.png

Downloads & links

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Map

FileDownload / File: emd_35931.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUfd4 without ARM domain in complex with Ubc4 at a resolution of 3.52 Angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.07266334 - 0.10517782
Average (Standard dev.)0.00008802486 (±0.0016634398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Ufd4 with ARM domain in complex with Ubc4...

Fileemd_35931_additional_1.map
AnnotationUfd4 with ARM domain in complex with Ubc4 at a resolution of 4.30 Angstrom
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ufd4 without ARM domain in complex with Ubc4-Ub...

Fileemd_35931_additional_2.map
AnnotationUfd4 without ARM domain in complex with Ubc4-Ub at a resolution of 6.55 Angstrom
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35931_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35931_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ufd4 in complex with Ubc4-Ub

EntireName: Ufd4 in complex with Ubc4-Ub
Components
  • Complex: Ufd4 in complex with Ubc4-Ub
    • Complex: Ufd4
      • Protein or peptide: Ubiquitin fusion degradation protein 4
    • Complex: Ubc4
      • Protein or peptide: Ubiquitin-conjugating enzyme E2 4

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Supramolecule #1: Ufd4 in complex with Ubc4-Ub

SupramoleculeName: Ufd4 in complex with Ubc4-Ub / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #2: Ufd4

SupramoleculeName: Ufd4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: Ubc4

SupramoleculeName: Ubc4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: Ubiquitin fusion degradation protein 4

MacromoleculeName: Ubiquitin fusion degradation protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 168.026031 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MSENNSHNLD EHESHSENSD YMMDTQVEDD YDEDGHVQGE YSYYPDEDED EHMLSSVGSF EADDGEDDDN DYHHEDDSGL LYGYHRTQN GSDEDRNEEE DGLERSHDNN EFGSNPLHLP DILETFAQRL EQRRQTSEGL GQHPVGRTLP EILSMIGGRM E RSAESSAR ...String:
MSENNSHNLD EHESHSENSD YMMDTQVEDD YDEDGHVQGE YSYYPDEDED EHMLSSVGSF EADDGEDDDN DYHHEDDSGL LYGYHRTQN GSDEDRNEEE DGLERSHDNN EFGSNPLHLP DILETFAQRL EQRRQTSEGL GQHPVGRTLP EILSMIGGRM E RSAESSAR NERISKLIEN TGNASEDPYI AMESLKELSE NILMMNQMVV DRIIPMETLI GNIAAILSDK ILREELELQM QA CRCMYNL FEVCPESISI AVDEHVIPIL QGKLVEISYI DLAEQVLETV EYISRVHGRD ILKTGQLSIY VQFFDFLTIH AQR KAIAIV SNACSSIRTD DFKTIVEVLP TLKPIFSNAT DQPILTRLVN AMYGICGALH GVDKFETLFS LDLIERIVQL VSIQ DTPLE NKLKCLDILT VLAMSSDVLS RELREKTDIV DMATRSFQHY SKSPNAGLHE TLIYVPNSLL ISISRFIVVL FPPED ERIL SADKYTGNSD RGVISNQEKF DSLVQCLIPI LVEIYTNAAD FDVRRYVLIA LLRVVSCINN STAKAINDQL IKLIGS ILA QKETASNANG TYSSEAGTLL VGGLSLLDLI CKKFSELFFP SIKREGIFDL VKDLSVDFNN IDLKEDGNEN ISLSDEE GD LHSSIEECDE GDEEYDYEFT DMEIPDSVKP KKISIHIFRT LSLAYIKNKG VNLVNRVLSQ MNVEQEAITE ELHQIEGV V SILENPSTPD KTEEDWKGIW SVLKKCIFHE DFDVSGFEFT STGLASSITK RITSSTVSHF ILAKSFLEVF EDCIDRFLE ILQSALTRLE NFSIVDCGLH DGGGVSSLAK EIKIKLVYDG DASKDNIGTD LSSTIVSVHC IASFTSLNEF LRHRMVRMRF LNSLIPNLT SSSTEADREE EENCLDHMRK KNFDFFYDNE KVDMESTVFG VIFNTFVRRN RDLKTLWDDT HTIKFCKSLE G NNRESEAA EEANEGKKLR DFYKKREFAQ VDTGSSADIL TLLDFLHSCG VKSDSFINSK LSAKLARQLD EPLVVASGAL PD WSLFLTR RFPFLFPFDT RMLFLQCTSF GYGRLIQLWK NKSKGSKDLR NDEALQQLGR ITRRKLRISR KTIFATGLKI LSK YGSSPD VLEIEYQEEA GTGLGPTLEF YSVVSKYFAR KSLNMWRCNS YSYRSEMDVD TTDDYITTLL FPEPLNPFSN NEKV IELFG YLGTFVARSL LDNRILDFRF SKVFFELLHR MSTPNVTTVP SDVETCLLMI ELVDPLLAKS LKYIVANKDD NMTLE SLSL TFTVPGNDDI ELIPGGCNKS LNSSNVEEYI HGVIDQILGK GIEKQLKAFI EGFSKVFSYE RMLILFPDEL VDIFGR VEE DWSMATLYTN LNAEHGYTMD SSIIHDFISI ISAFGKHERR LFLQFLTGSP KLPIGGFKSL NPKFTVVLKH AEDGLTA DE YLPSVMTCAN YLKLPKYTSK DIMRSRLCQA IEEGAGAFLL S

UniProtKB: Ubiquitin fusion degradation protein 4

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Macromolecule #2: Ubiquitin-conjugating enzyme E2 4

MacromoleculeName: Ubiquitin-conjugating enzyme E2 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.442586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSSSKRIAKE LSDLERDPPT SSSAGPVGDD LYHWQASIMG PADSPYAGGV FFLSIHFPTD YPFKPPKISF TTKIYHPNIN ANGNICLDI LKDQWSPALT LSKVLLSISS LLTDANPDDP LVPEIAHIYK TDRPKYEATA REWTKKYAV

UniProtKB: Ubiquitin-conjugating enzyme E2 4

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.347 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: NONE
Details: The initial model was generated form Initial Model section on RELION3.1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124116
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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