cryo-EM structures of Ufd4 in complex with Ubc4-Ub. Determined by electron microscopy at 3.52 Å resolution. Released 17 Apr 2024.
Explore 8J1R in 3D Show helices and sheets RCSB PDB PDBe
8J1R contains 48 α-helices and 30 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 711-725 | 15 | |
| α-helix | 734-748 | 15 | |
| β-strand | 749 | 1 | 1 |
| β-strand | 754 | 1 | 1 |
| α-helix | 755-756 | 2 | |
| α-helix | 757-762 | 6 | |
| α-helix | 765-774 | 10 | |
| α-helix | 780-791 | 12 | |
| α-helix | 795-809 | 15 | |
| α-helix | 825-827 | 3 | |
| β-strand | 832-838 | 7 | 2 |
| β-strand | 853-858 | 6 | 2 |
| β-strand | 863 | 1 | 3 |
| β-strand | 914-915 | 2 | 2 |
| β-strand | 920-921 | 2 | 2 |
| β-strand | 926 | 1 | 3 |
| α-helix | 927-937 | 11 | |
| β-strand | 950-954 | 5 | 2 |
| α-helix | 992-994 | 3 | |
| α-helix | 995-1006 | 12 | |
| α-helix | 1017-1028 | 12 | |
| α-helix | 1030-1034 | 5 | |
| α-helix | 1040-1048 | 9 | |
| α-helix | 1050-1052 | 3 | |
| α-helix | 1055-1065 | 11 | |
| α-helix | 1069-1081 | 13 | |
| α-helix | 1090-1095 | 6 | |
| β-strand | 1100-1105 | 6 | 4 |
| α-helix | 1110-1120 | 11 | |
| β-strand | 1127-1132 | 6 | 4 |
| α-helix | 1140-1153 | 14 | |
| β-strand | 1156 | 1 | 5 |
| β-strand | 1162 | 1 | 6 |
| β-strand | 1181 | 1 | 5 |
| β-strand | 1186 | 1 | 7 |
| β-strand | 1188 | 1 | 6 |
| α-helix | 1190-1192 | 3 | |
| α-helix | 1198-1216 | 19 | |
| β-strand | 1225 | 1 | 7 |
| α-helix | 1227-1237 | 11 | |
| α-helix | 1248-1255 | 8 | |
| α-helix | 1260-1271 | 12 | |
| α-helix | 1276-1282 | 7 | |
| β-strand | 1285 | 1 | 8 |
| β-strand | 1287 | 1 | 9 |
| β-strand | 1295 | 1 | 9 |
| α-helix | 1303 | 1 | |
| β-strand | 1304 | 1 | 8 |
| α-helix | 1305 | 1 | |
| α-helix | 1307-1309 | 3 | |
| α-helix | 1310-1321 | 12 | |
| α-helix | 1324-1338 | 15 | |
| α-helix | 1343-1348 | 6 | |
| α-helix | 1351-1358 | 8 | |
| α-helix | 1367-1372 | 6 | |
| β-strand | 1375-1377 | 3 | 10 |
| α-helix | 1385-1395 | 11 | |
| α-helix | 1400-1409 | 10 | |
| α-helix | 1415-1416 | 2 | |
| α-helix | 1420-1422 | 3 | |
| β-strand | 1428-1432 | 5 | 10 |
| α-helix | 1443-1445 | 3 | |
| β-strand | 1453-1457 | 5 | 10 |
| α-helix | 1462-1475 | 14 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 3-16 | 14 | |
| β-strand | 23-26 | 4 | 11 |
| β-strand | 33-39 | 7 | 11 |
| β-strand | 50-56 | 7 | 11 |
| α-helix | 65-66 | 2 | |
| β-strand | 67-70 | 4 | 11 |
| β-strand | 79 | 1 | 12 |
| β-strand | 85 | 1 | 12 |
| α-helix | 100-110 | 11 | |
| α-helix | 122-128 | 7 | |
| α-helix | 133-135 | 3 | |
| α-helix | 136-140 | 5 | |
| α-helix | 141-142 | 2 | |
| α-helix | 143-147 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Ubiquitin fusion degradation protein 4 | A | protein | 1483 | Saccharomyces cerevisiae | P33202 (AlphaFold model) |
| Ubiquitin-conjugating enzyme E2 4 | C | protein | 148 | Saccharomyces cerevisiae | P15731 (AlphaFold model) |
>8J1R_1 Ubiquitin fusion degradation protein 4 (chains A) MSENNSHNLDEHESHSENSDYMMDTQVEDDYDEDGHVQGEYSYYPDEDEDEHMLSSVGSF EADDGEDDDNDYHHEDDSGLLYGYHRTQNGSDEDRNEEEDGLERSHDNNEFGSNPLHLPD ILETFAQRLEQRRQTSEGLGQHPVGRTLPEILSMIGGRMERSAESSARNERISKLIENTG NASEDPYIAMESLKELSENILMMNQMVVDRIIPMETLIGNIAAILSDKILREELELQMQA CRCMYNLFEVCPESISIAVDEHVIPILQGKLVEISYIDLAEQVLETVEYISRVHGRDILK TGQLSIYVQFFDFLTIHAQRKAIAIVSNACSSIRTDDFKTIVEVLPTLKPIFSNATDQPI LTRLVNAMYGICGALHGVDKFETLFSLDLIERIVQLVSIQDTPLENKLKCLDILTVLAMS SDVLSRELREKTDIVDMATRSFQHYSKSPNAGLHETLIYVPNSLLISISRFIVVLFPPED ERILSADKYTGNSDRGVISNQEKFDSLVQCLIPILVEIYTNAADFDVRRYVLIALLRVVS CINNSTAKAINDQLIKLIGSILAQKETASNANGTYSSEAGTLLVGGLSLLDLICKKFSEL FFPSIKREGIFDLVKDLSVDFNNIDLKEDGNENISLSDEEGDLHSSIEECDEGDEEYDYE FTDMEIPDSVKPKKISIHIFRTLSLAYIKNKGVNLVNRVLSQMNVEQEAITEELHQIEGV VSILENPSTPDKTEEDWKGIWSVLKKCIFHEDFDVSGFEFTSTGLASSITKRITSSTVSH FILAKSFLEVFEDCIDRFLEILQSALTRLENFSIVDCGLHDGGGVSSLAKEIKIKLVYDG DASKDNIGTDLSSTIVSVHCIASFTSLNEFLRHRMVRMRFLNSLIPNLTSSSTEADREEE ENCLDHMRKKNFDFFYDNEKVDMESTVFGVIFNTFVRRNRDLKTLWDDTHTIKFCKSLEG NNRESEAAEEANEGKKLRDFYKKREFAQVDTGSSADILTLLDFLHSCGVKSDSFINSKLS AKLARQLDEPLVVASGALPDWSLFLTRRFPFLFPFDTRMLFLQCTSFGYGRLIQLWKNKS KGSKDLRNDEALQQLGRITRRKLRISRKTIFATGLKILSKYGSSPDVLEIEYQEEAGTGL GPTLEFYSVVSKYFARKSLNMWRCNSYSYRSEMDVDTTDDYITTLLFPEPLNPFSNNEKV IELFGYLGTFVARSLLDNRILDFRFSKVFFELLHRMSTPNVTTVPSDVETCLLMIELVDP LLAKSLKYIVANKDDNMTLESLSLTFTVPGNDDIELIPGGCNKSLNSSNVEEYIHGVIDQ ILGKGIEKQLKAFIEGFSKVFSYERMLILFPDELVDIFGRVEEDWSMATLYTNLNAEHGY TMDSSIIHDFISIISAFGKHERRLFLQFLTGSPKLPIGGFKSLNPKFTVVLKHAEDGLTA DEYLPSVMTCANYLKLPKYTSKDIMRSRLCQAIEEGAGAFLLS
>8J1R_2 Ubiquitin-conjugating enzyme E2 4 (chains C) MSSSKRIAKELSDLERDPPTSSSAGPVGDDLYHWQASIMGPADSPYAGGVFFLSIHFPTD YPFKPPKISFTTKIYHPNINANGNICLDILKDQWSPALTLSKVLLSISSLLTDANPDDPL VPEIAHIYKTDRPKYEATAREWTKKYAV
Structural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination. Wu, X., Ai, H., Mao, J. et al. Nat Commun (2025) 16:4313-4313. DOI 10.1038/s41467-025-59569-6 · PubMed
Other PDB entries of the same protein (UniProt P33202 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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