9KHT: Ufd2/Ubc4-Ub
cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation). Determined by electron microscopy at 4.85 Å resolution. Released 30 Jul 2025.
- Method
- Electron microscopy
- Resolution
- 4.85 Å
- Organisms
- Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 12
- Atoms
- 19,960
- Mol. weight
- 320.17 kDa
- Released
- 30 Jul 2025
Explore 9KHT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9KHT contains 151 α-helices and 92 β-strands across 12 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: 54 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-7 | 6 | |
| β-strand | 10-11 | 2 | 28 |
| α-helix | 20 | 1 | |
| β-strand | 21-22 | 2 | 28 |
| α-helix | 36-38 | 3 | |
| α-helix | 39-48 | 10 | |
| α-helix | 56-75 | 20 | |
| α-helix | 84-101 | 18 | |
| α-helix | 113-122 | 10 | |
| α-helix | 124-141 | 18 | |
| α-helix | 145-150 | 6 | |
| α-helix | 156-160 | 5 | |
| α-helix | 174-186 | 13 | |
| α-helix | 188-194 | 7 | |
| α-helix | 208-210 | 3 | |
| α-helix | 228-234 | 7 | |
| α-helix | 243-272 | 30 | |
| α-helix | 276-291 | 16 | |
| α-helix | 294-297 | 4 | |
| α-helix | 303-305 | 3 | |
| α-helix | 309-319 | 11 | |
| α-helix | 320-322 | 3 | |
| α-helix | 323-326 | 4 | |
| α-helix | 334-336 | 3 | |
| α-helix | 339-342 | 4 | |
| α-helix | 345-346 | 2 | |
| β-strand | 356 | 1 | 29 |
| α-helix | 361-371 | 11 | |
| α-helix | 381-392 | 12 | |
| α-helix | 393-398 | 6 | |
| α-helix | 399-422 | 24 | |
| α-helix | 431-460 | 30 | |
| α-helix | 465-484 | 20 | |
| α-helix | 520 | 1 | |
| α-helix | 523-525 | 3 | |
| β-strand | 527 | 1 | 29 |
| α-helix | 529-541 | 13 | |
| α-helix | 557-565 | 9 | |
| α-helix | 569-571 | 3 | |
| α-helix | 575-589 | 15 | |
| α-helix | 596-598 | 3 | |
| α-helix | 601-605 | 5 | |
| α-helix | 608-611 | 4 | |
| α-helix | 614-624 | 11 | |
| α-helix | 625-627 | 3 | |
| α-helix | 637-654 | 18 | |
| α-helix | 656-668 | 13 | |
| α-helix | 670-704 | 35 | |
| α-helix | 720-754 | 35 | |
| α-helix | 756-759 | 4 | |
| α-helix | 762-780 | 19 | |
| α-helix | 782-786 | 5 | |
| α-helix | 799-813 | 15 | |
| α-helix | 817-824 | 8 | |
| α-helix | 832-844 | 13 | |
| α-helix | 851-876 | 26 | |
| β-strand | 886 | 1 | 30 |
| β-strand | 893 | 1 | 30 |
| β-strand | 897-899 | 3 | 31 |
| β-strand | 906-908 | 3 | 31 |
| α-helix | 909-918 | 10 | |
| β-strand | 921 | 1 | 32 |
| β-strand | 928 | 1 | 32 |
| β-strand | 935-936 | 2 | 31 |
| α-helix | 938-954 | 17 | |
Chain A: 56 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-7 | 6 | |
| β-strand | 10-11 | 2 | 22 |
| α-helix | 20 | 1 | |
| β-strand | 21-22 | 2 | 22 |
| α-helix | 36-38 | 3 | |
| α-helix | 39-47 | 9 | |
| α-helix | 56-75 | 20 | |
| α-helix | 84-101 | 18 | |
| α-helix | 113-122 | 10 | |
| α-helix | 124-127 | 4 | |
| α-helix | 130-141 | 12 | |
| α-helix | 145-157 | 13 | |
| α-helix | 158-162 | 5 | |
| α-helix | 174-184 | 11 | |
| α-helix | 188-194 | 7 | |
| α-helix | 208-211 | 4 | |
| α-helix | 228-235 | 8 | |
| α-helix | 243-272 | 30 | |
| α-helix | 276-291 | 16 | |
| α-helix | 294-297 | 4 | |
| α-helix | 303-305 | 3 | |
| α-helix | 309-319 | 11 | |
| α-helix | 320-322 | 3 | |
| α-helix | 323-326 | 4 | |
| α-helix | 334-336 | 3 | |
| α-helix | 339-342 | 4 | |
| α-helix | 345-346 | 2 | |
| β-strand | 356 | 1 | 23 |
| α-helix | 361-371 | 11 | |
| α-helix | 381-393 | 13 | |
| α-helix | 394-398 | 5 | |
| α-helix | 399-405 | 7 | |
| α-helix | 407-416 | 10 | |
| α-helix | 431-460 | 30 | |
| α-helix | 463-484 | 22 | |
| α-helix | 520 | 1 | |
| α-helix | 523-525 | 3 | |
| β-strand | 527 | 1 | 23 |
| α-helix | 529-541 | 13 | |
| α-helix | 557-565 | 9 | |
| α-helix | 575-589 | 15 | |
| α-helix | 596-598 | 3 | |
| α-helix | 601-605 | 5 | |
| α-helix | 608-611 | 4 | |
| α-helix | 614-624 | 11 | |
| α-helix | 625-627 | 3 | |
| α-helix | 637-651 | 15 | |
| α-helix | 656-668 | 13 | |
| α-helix | 670-704 | 35 | |
| α-helix | 720-754 | 35 | |
| α-helix | 756-759 | 4 | |
| α-helix | 762-780 | 19 | |
| α-helix | 782-786 | 5 | |
| α-helix | 799-813 | 15 | |
| α-helix | 817-824 | 8 | |
| α-helix | 833-844 | 12 | |
| α-helix | 851-876 | 26 | |
| β-strand | 886 | 1 | 24 |
| β-strand | 893 | 1 | 24 |
| β-strand | 897-899 | 3 | 25 |
| β-strand | 906-908 | 3 | 25 |
| α-helix | 909-916 | 8 | |
| α-helix | 931-933 | 3 | |
| β-strand | 935-936 | 2 | 25 |
| α-helix | 938-954 | 17 | |
Chain b: 6 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-16 | 12 | |
| β-strand | 22-23 | 2 | 33 |
| β-strand | 33-34 | 2 | 34 |
| β-strand | 37-39 | 3 | 33 |
| β-strand | 50-52 | 3 | 33 |
| β-strand | 53-56 | 4 | 34 |
| α-helix | 65-67 | 3 | |
| β-strand | 68-70 | 3 | 34 |
| α-helix | 88-91 | 4 | |
| α-helix | 100-108 | 9 | |
| α-helix | 122-130 | 9 | |
| α-helix | 132-145 | 14 | |
Chain B: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-16 | 12 | |
| β-strand | 26 | 1 | 26 |
| β-strand | 34 | 1 | 26 |
| β-strand | 53-56 | 4 | 27 |
| α-helix | 61-63 | 3 | |
| α-helix | 65-66 | 2 | |
| β-strand | 67-70 | 4 | 27 |
| α-helix | 88-92 | 5 | |
| α-helix | 100-108 | 9 | |
| α-helix | 122-130 | 9 | |
| α-helix | 132-145 | 14 | |
Chain c: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 20 |
| β-strand | 12-16 | 5 | 20 |
| β-strand | 22 | 1 | 21 |
| α-helix | 23-27 | 5 | |
| α-helix | 38-40 | 3 | |
| β-strand | 43-45 | 3 | 20 |
| β-strand | 48-50 | 3 | 20 |
| β-strand | 55 | 1 | 21 |
| α-helix | 56-59 | 4 | |
| β-strand | 67-69 | 3 | 20 |
Chain C: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 18 |
| β-strand | 12-15 | 4 | 18 |
| β-strand | 22 | 1 | 19 |
| α-helix | 23-27 | 5 | |
| α-helix | 38-40 | 3 | |
| β-strand | 43-45 | 3 | 18 |
| β-strand | 48-50 | 3 | 18 |
| β-strand | 55 | 1 | 19 |
| α-helix | 56-59 | 4 | |
| α-helix | 65-66 | 2 | |
| β-strand | 67-69 | 3 | 18 |
Chain d: 4 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 10 |
| β-strand | 6 | 1 | 11 |
| β-strand | 12 | 1 | 11 |
| β-strand | 15-16 | 2 | 10 |
| β-strand | 22 | 1 | 12 |
| α-helix | 23-27 | 5 | |
| α-helix | 31-34 | 4 | |
| α-helix | 38-40 | 3 | |
| β-strand | 42-45 | 4 | 13 |
| β-strand | 48-49 | 2 | 13 |
| β-strand | 55 | 1 | 12 |
| α-helix | 56-59 | 4 | |
| β-strand | 68-70 | 3 | 13 |
Chain D: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 1 |
| β-strand | 4 | 1 | 2 |
| β-strand | 6 | 1 | 3 |
| β-strand | 12 | 1 | 3 |
| β-strand | 15-16 | 2 | 1 |
| β-strand | 22 | 1 | 4 |
| α-helix | 23-27 | 5 | |
| α-helix | 31-34 | 4 | |
| α-helix | 38-40 | 3 | |
| β-strand | 42-45 | 4 | 5 |
| β-strand | 48-49 | 2 | 5 |
| β-strand | 55 | 1 | 4 |
| α-helix | 56-58 | 3 | |
| β-strand | 66 | 1 | 2 |
| β-strand | 68-70 | 3 | 5 |
4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Polyubiquitin-C | D, d | protein | 76 | Homo sapiens | P0CG48 (AlphaFold model) |
| Ubiquitin | C, E, F, c, e, f | protein | 76 | Homo sapiens | P62979 (AlphaFold model) |
| E4 ubiquitin-protein ligase UFD2 | A, a | protein | 955 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P54860 (AlphaFold model) |
| Ubiquitin-conjugating enzyme E2 4 | B, b | protein | 148 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P15731 (AlphaFold model) |
Sequence of entity 1 (D, d), FASTA
>9KHT_1 Polyubiquitin-C (chains D, d)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGCQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 2 (C, E, F, c, e, f), FASTA
>9KHT_2 Ubiquitin (chains C, E, F, c, e, f)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 3 (A, a), FASTA
>9KHT_3 E4 ubiquitin-protein ligase UFD2 (chains A, a)
MTAIEDILQITTDPSDTRGYSLLKSEEVPQGSTLGVDFIDTLLLYQLTENEKLDKPFEYL
NDCFRRNQQQKRITKNKPNAESLHSTFQEIDRLVIGYGVVALQIENFCMNGAFINYITGI
VSNVNSYTDFLSQIIQRAILEGTALDLLNAVFPTLLEYCNKHVSHFDLNESVIYNNVLTI
FELFVTFKPIAEIFTKIDGFFADYSCKPQDFERKTILGPILSLSPIEAAVAIRNYGDNLL
RSKQQTAMIHESLQAEHKVVIDRLFFIVDKLVRGSLNSRTDMISYFAHIANKNHLRRADH
PPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDKIDANYFNNPSLFIDLSGETRLNSD
FKEADAFYDKNRKTADSKPNFISDCFFLTLTYLHYGLGGTLSFEEKMGSEIKALKEEIEK
VKKIAANHDVFARFITAQLSKMEKALKTTESLRFALQGFFAHRSLQLEVFDFICGASTFL
IRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHAPVPFKYYPEFVVEGPVNYSLY
ISKYQTSPIFRNPRLGSFVEFTTMVLRCPELVSNPHLKGKLVQLLSVGAMPLTDNSPGFM
MDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYYKIPSYKN
QLIWQSQNNADFFVRFVARMLNDLTFLLDEGLSNLAEVHNIQNELDNRARGAPPTREEED
KELQTRLASASRQAKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLNYNLESLV
GPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFVRAVD
ILGRKTGLASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVIL
PASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILCFKKQKKEEA
Sequence of entity 4 (B, b), FASTA
>9KHT_4 Ubiquitin-conjugating enzyme E2 4 (chains B, b)
MSSSKRIAKELSDLERDPPTSSSAGPVGDDLYHWQASIMGPADSPYAGGVFFLSIHFPTD
YPFKPPKISFTTKIYHPNINANGNICLDILKDQWSPALTLSKVLLSISSLLTDANPDDPL
VPEIAHIYKTDRPKYEATAREWTKKYAV
Primary citation
Structural basis for E4 enzyme Ufd2-catalyzed K48/K29 branched ubiquitin chains. Tong, Z., Wu, X., Cai, H. et al. Nat Chem Biol (2026) 22:239-248. DOI 10.1038/s41589-025-01985-2 · PubMed
Other PDB entries of the same protein (UniProt P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
- 1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
- 5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
- 2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
- 4HK2 1.4 Å, U7Ub25.2540
- 9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
- 1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
- 4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
- 7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
- 5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
- 9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
- 9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant
Browse structure collections
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