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- EMDB-62353: Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb... -

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Basic information

Entry
Database: EMDB / ID: EMD-62353
TitleCryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation)
Map data
Sample
  • Complex: Ufd2/Ufd4-Ub in complex with K29-linked diUb
    • Protein or peptide: E4 ubiquitin-protein ligase UFD2
    • Protein or peptide: Polyubiquitin-C
    • Protein or peptide: Polyubiquitin-C
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 4
KeywordsE4 enzyme / Ub ligase / Ufd2 / Ubc4 / Branching / K48/29 / LIGASE
Function / homology
Function and homology information


Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / ribosome-associated ubiquitin-dependent protein catabolic process / Formation of the ternary complex, and subsequently, the 43S complex / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme ...Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / ribosome-associated ubiquitin-dependent protein catabolic process / Formation of the ternary complex, and subsequently, the 43S complex / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / Ribosomal scanning and start codon recognition / Translation initiation complex formation / proteasome binding / ubiquitin conjugating enzyme activity / SARS-CoV-1 modulates host translation machinery / cellular response to ethanol / Peptide chain elongation / Antigen processing: Ubiquitination & Proteasome degradation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / ubiquitin ligase complex / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein K48-linked ubiquitination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ERAD pathway / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / cytosolic ribosome / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / rescue of stalled ribosome / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D
Similarity search - Function
Ubiquitin conjugation factor E4, core / Ubiquitin conjugation factor E4 / Ubiquitin elongating factor core / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 ...Ubiquitin conjugation factor E4, core / Ubiquitin conjugation factor E4 / Ubiquitin elongating factor core / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / 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 / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 4 / E4 ubiquitin-protein ligase UFD2 / Ubiquitin-ribosomal protein eS31 fusion protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.31 Å
AuthorsAi HS / Tong ZB / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810, 22407121, T2488301, 22277073 and 92253302, China
CitationJournal: To Be Published
Title: Structural basis for the ubiquitin E4 enzyme Ufd2-catalyzed K48/K29 branched ubiquitin chains
Authors: Tong ZB / Ai HS / Liu L
History
DepositionNov 11, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62353.png

Downloads & links

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Map

FileDownload / File: emd_62353.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 219.58 Å		1.1 Å/pix.
x 200 pix.
= 219.58 Å		1.1 Å/pix.
x 200 pix.
= 219.58 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0165
Minimum - Maximum-0.16113347 - 0.18155321
Average (Standard dev.)0.000016348824 (±0.004643087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 219.58 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62353_msk_1.map
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Additional map: #2

Fileemd_62353_additional_1.map
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Additional map: #1

Fileemd_62353_additional_2.map
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Half map: #2

Fileemd_62353_half_map_1.map
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Half map: #1

Fileemd_62353_half_map_2.map
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Sample components

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Entire : Ufd2/Ufd4-Ub in complex with K29-linked diUb

EntireName: Ufd2/Ufd4-Ub in complex with K29-linked diUb
Components
  • Complex: Ufd2/Ufd4-Ub in complex with K29-linked diUb
    • Protein or peptide: E4 ubiquitin-protein ligase UFD2
    • Protein or peptide: Polyubiquitin-C
    • Protein or peptide: Polyubiquitin-C
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 4

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Supramolecule #1: Ufd2/Ufd4-Ub in complex with K29-linked diUb

SupramoleculeName: Ufd2/Ufd4-Ub in complex with K29-linked diUb / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #5, #2-#4, #1
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Macromolecule #1: Ubiquitin-conjugating enzyme E2 4

MacromoleculeName: Ubiquitin-conjugating enzyme E2 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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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Macromolecule #2: Polyubiquitin-C

MacromoleculeName: Polyubiquitin-C / type: protein_or_peptide / ID: 2 / Details: K29diUb (proximal Ub) / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.665881 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGCQL EDGRTLSDYN IQKESTLHLV LRLRGGD

UniProtKB: Polyubiquitin-C

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Macromolecule #3: Polyubiquitin-C

MacromoleculeName: Polyubiquitin-C / type: protein_or_peptide / ID: 3 / Details: K29diUb (distal Ub) / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.604845 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKARI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-C

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Macromolecule #4: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 4 / Details: K48Ub (Donor Ubiquitin) / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Ubiquitin-ribosomal protein eS31 fusion protein

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Macromolecule #5: E4 ubiquitin-protein ligase UFD2

MacromoleculeName: E4 ubiquitin-protein ligase UFD2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 110.044523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTAIEDILQI TTDPSDTRGY SLLKSEEVPQ GSTLGVDFID TLLLYQLTEN EKLDKPFEYL NDCFRRNQQQ KRITKNKPNA ESLHSTFQE IDRLVIGYGV VALQIENFCM NGAFINYITG IVSNVNSYTD FLSQIIQRAI LEGTALDLLN AVFPTLLEYC N KHVSHFDL ...String:
MTAIEDILQI TTDPSDTRGY SLLKSEEVPQ GSTLGVDFID TLLLYQLTEN EKLDKPFEYL NDCFRRNQQQ KRITKNKPNA ESLHSTFQE IDRLVIGYGV VALQIENFCM NGAFINYITG IVSNVNSYTD FLSQIIQRAI LEGTALDLLN AVFPTLLEYC N KHVSHFDL NESVIYNNVL TIFELFVTFK PIAEIFTKID GFFADYSCKP QDFERKTILG PILSLSPIEA AVAIRNYGDN LL RSKQQTA MIHESLQAEH KVVIDRLFFI VDKLVRGSLN SRTDMISYFA HIANKNHLRR ADHPPFKELS SNGFMSNITL LLV RFSQPF LDISYKKIDK IDANYFNNPS LFIDLSGETR LNSDFKEADA FYDKNRKTAD SKPNFISDCF FLTLTYLHYG LGGT LSFEE KMGSEIKALK EEIEKVKKIA ANHDVFARFI TAQLSKMEKA LKTTESLRFA LQGFFAHRSL QLEVFDFICG ASTFL IRVV DPEHEFPFKQ IKLPLIPDQI GVENVDNADF LRAHAPVPFK YYPEFVVEGP VNYSLYISKY QTSPIFRNPR LGSFVE FTT MVLRCPELVS NPHLKGKLVQ LLSVGAMPLT DNSPGFMMDI FEHDELVNKN LLYALLDFYV IVEKTGSSSQ FYDKFNS RY SISIILEELY YKIPSYKNQL IWQSQNNADF FVRFVARMLN DLTFLLDEGL SNLAEVHNIQ NELDNRARGA PPTREEED K ELQTRLASAS RQAKSSCGLA DKSMKLFEIY SKDIPAAFVT PEIVYRLASM LNYNLESLVG PKCGELKVKD PQSYSFNPK DLLKALTTVY INLSEQSEFI SAVAKDERSF NRNLFVRAVD ILGRKTGLAS PEFIEKLLNF ANKAEEQRKA DEEEDLEYGD VPDEFLDPL MYTIMKDPVI LPASKMNIDR STIKAHLLSD STDPFNRMPL KLEDVTPNEE LRQKILCFKK QKKEEAKHKA S E

UniProtKB: E4 ubiquitin-protein ligase UFD2

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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: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 191564
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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