8J1P: Ufd4

Cryo-EM structure of Ufd4 in complex with K29/48 triUb. Determined by electron microscopy at 3.31 Å resolution. Released 17 Apr 2024.

Method
Electron microscopy
Resolution
3.31 Å
Organisms
Saccharomyces cerevisiae, Homo sapiens
Chains
4
Atoms
11,523
Mol. weight
193.73 kDa
Released
17 Apr 2024

Explore 8J1P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J1P contains 83 α-helices and 45 β-strands across 4 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.

Chain A: 77 helices, 26 β-strands

ElementResiduesLengthSheet
α-helix165-18016
α-helix181-1833
α-helix188-20114
α-helix205-2095
α-helix214-22613
α-helix234-25017
α-helix254-2596
α-helix263-27210
α-helix277-29115
α-helix295-3017
α-helix311-3133
α-helix317-32913
α-helix335-3373
α-helix338-35316
α-helix358-3614
α-helix364-37512
α-helix387-3959
α-helix404-41916
α-helix423-4308
α-helix435-4439
α-helix453-4597
α-helix462-47413
β-strand48511
α-helix505-52016
α-helix525-53814
α-helix544-5474
α-helix548-5503
α-helix551-56111
α-helix565-5684
β-strand56912
β-strand57512
α-helix577-59620
α-helix598-60811
α-helix611-62313
α-helix665-6673
α-helix671-6733
β-strand68011
α-helix682-6843
α-helix685-70117
α-helix713-72513
α-helix734-74815
β-strand74913
β-strand75413
α-helix757-7626
α-helix765-77511
α-helix780-79011
α-helix795-80915
α-helix812-8154
α-helix825-8273
β-strand831-83554
β-strand837-83825
β-strand855-85954
β-strand86316
α-helix864-87512
α-helix906-9094
β-strand91317
β-strand92616
α-helix929-9379
α-helix942-9476
β-strand95014
β-strand953-95425
β-strand95517
α-helix975-9762
α-helix979-9813
α-helix992-9943
α-helix995-100511
α-helix1017-102711
α-helix1030-10334
α-helix1040-10489
α-helix1055-106612
α-helix1069-10713
β-strand1100-110568
α-helix1107-11093
α-helix1110-112112
β-strand1127-113268
α-helix1140-115314
β-strand115619
α-helix1157-11593
β-strand1162110
β-strand118119
β-strand1188110
α-helix1200-121617
α-helix1227-123711
α-helix1249-12557
α-helix1260-127112
α-helix1276-12827
β-strand1287111
β-strand1295111
α-helix1310-132112
α-helix1327-134014
α-helix1343-13486
α-helix1351-13533
α-helix13551
α-helix1356-13605
α-helix1361-13644
α-helix1367-13715
α-helix1388-13947
α-helix1399-140911
α-helix1420-14223
β-strand1429-1432412
β-strand1446112
β-strand1454-1457412
α-helix1462-147615
Chain C: 2 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand4-6313
β-strand12-14313
β-strand22114
α-helix23-3412
α-helix38-403
β-strand42-44313
β-strand49113
β-strand55114
β-strand66-70513
Chain D: 2 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand4-6315
β-strand12-14315
α-helix24-3310
α-helix38-403
β-strand42-45415
β-strand48-49215
β-strand66-70515
Chain E: 2 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand2-6516
β-strand12-16516
β-strand22117
α-helix25-339
α-helix38-403
β-strand42-44316
β-strand49116
β-strand55117
β-strand66-70516

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Ubiquitin fusion degradation protein 4Aprotein1483Saccharomyces cerevisiaeP33202 (AlphaFold model)
UbiquitinC, Eprotein76Homo sapiensP0CG47 (AlphaFold model)
UbiquitinDprotein76Homo sapiensP0CG47 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8J1P_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
Sequence of entity 2 (C, E), FASTA
>8J1P_2 Ubiquitin (chains C, E)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 3 (D), FASTA
>8J1P_3 Ubiquitin (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKACIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

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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