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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 / cytoplasm protein quality control by the ubiquitin-proteasome system / protein K29-linked ubiquitination / mitochondria-associated ubiquitin-dependent protein catabolic process / free ubiquitin chain polymerization / Antigen processing: Ubiquitination & Proteasome degradation / HECT-type E3 ubiquitin transferase / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Transferases; Acyltransferases; Aminoacyltransferases ...proteasome regulatory particle binding / Peroxisomal protein import / cytoplasm protein quality control by the ubiquitin-proteasome system / protein K29-linked ubiquitination / mitochondria-associated ubiquitin-dependent protein catabolic process / free ubiquitin chain polymerization / Antigen processing: Ubiquitination & Proteasome degradation / HECT-type E3 ubiquitin transferase / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Transferases; Acyltransferases; Aminoacyltransferases / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / proteasome binding / protein monoubiquitination / ubiquitin conjugating enzyme activity / rescue of stalled ribosome / ubiquitin ligase complex / ubiquitin binding / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear speck / ubiquitin protein ligase binding / 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, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 ...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, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / 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: To Be Published
Title: Structural Visualization of HECT-E3 Ufd4 accepting and transferring Ubiquitin to Form K29/K48-branched Polyubiquitination on N-degron. bioRxiv,doi: ttps://doi.org/10.1101/2023.05.23.542033
Authors: Mao JX / Ai HS / Wu XW / Cai HY / Pan M / Liu L
History
DepositionApr 13, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing 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
Voxel sizeX=Y=Z: 1.074 Å
Density
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

Projections

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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.347 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Details: The initial model was generated form Initial Model section on RELION3.1
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124116

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