9KHS: Ufd2/Ubc4-Ub

Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation). Determined by electron microscopy at 4.31 Å resolution. Released 30 Jul 2025.

Method: Electron microscopy
Resolution: 4.31 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains: 5
Atoms: 9,327
Mol. weight: 152.33 kDa
Released: 30 Jul 2025

Explore 9KHS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KHS contains 61 α-helices and 36 β-strands across 5 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: 49 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	118-122	5
α-helix	127-130	4
α-helix	132-139	8
α-helix	144-157	14
α-helix	158-162	5
α-helix	173-185	13
α-helix	188-191	4
α-helix	194-196	3
α-helix	208-210	3
α-helix	218-221	4
α-helix	228-234	7
α-helix	243-272	30
α-helix	276-291	16
α-helix	294-297	4
α-helix	309-323	15
α-helix	333-336	4
α-helix	345-346	2
α-helix	354-355	2
β-strand	356	1	10
α-helix	361-369	9
α-helix	381-392	12
α-helix	393-397	5
α-helix	398-405	8
α-helix	407-421	15
α-helix	429-461	33
α-helix	463-484	22
α-helix	521-524	4
β-strand	527	1	10
α-helix	529-541	13
α-helix	553-555	3
α-helix	556-567	12
α-helix	575-588	14
α-helix	596-598	3
α-helix	601-605	5
α-helix	610-624	15
α-helix	639-654	16
α-helix	656-668	13
α-helix	670-702	33
α-helix	721-754	34
α-helix	756-759	4
α-helix	762-780	19
α-helix	782-786	5
α-helix	792-795	4
α-helix	799-812	14
α-helix	817-824	8
α-helix	832-844	13
α-helix	851-876	26
α-helix	883-885	3
β-strand	886	1	11
β-strand	893	1	11
β-strand	897-899	3	12
β-strand	906-908	3	12
α-helix	909-916	8
β-strand	921	1	13
β-strand	928	1	13
α-helix	931-933	3
β-strand	935-936	2	12
α-helix	938-952	15

Chain B: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
β-strand	22-27	6	1
β-strand	30-39	10	1
β-strand	50-56	7	1
α-helix	61-63	3
β-strand	67-70	4	1
β-strand	79	1	2
β-strand	85	1	2
α-helix	88-90	3
α-helix	100-113	14
α-helix	122-128	7
α-helix	132-145	14

Chain C: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	12-15	4	6
β-strand	22	1	7
α-helix	23-27	5
α-helix	38-40	3
β-strand	43	1	8
β-strand	44-45	2	9
β-strand	48-49	2	9
β-strand	55	1	7
α-helix	56-58	3
β-strand	66-68	3	6
β-strand	69	1	8

Chain D: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-32	10
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50	1
β-strand	55	1	4
β-strand	66-71	6	3

Chain E: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	5
β-strand	12-16	5	5
α-helix	23-34	12
β-strand	41-45	5	5
β-strand	48-49	2	5
β-strand	66-71	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 4	B	protein	148	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P15731 (AlphaFold model)
Polyubiquitin-C	D	protein	77	Homo sapiens	P0CG48 (AlphaFold model)
Polyubiquitin-C	E	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin	C	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
E4 ubiquitin-protein ligase UFD2	A	protein	961	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P54860 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9KHS_1 Ubiquitin-conjugating enzyme E2 4 (chains B)
MSSSKRIAKELSDLERDPPTSSSAGPVGDDLYHWQASIMGPADSPYAGGVFFLSIHFPTD
YPFKPPKISFTTKIYHPNINANGNICLDILKDQWSPALTLSKVLLSISSLLTDANPDDPL
VPEIAHIYKTDRPKYEATAREWTKKYAV

Sequence of entity 2 (D), FASTA

>9KHS_2 Polyubiquitin-C (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGCQLEDGRTLSDYN
IQKESTLHLVLRLRGGD

Sequence of entity 3 (E), FASTA

>9KHS_3 Polyubiquitin-C (chains E)
MQIFVKTLTGKTITLEVEPSDTIENVKARIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 4 (C), FASTA

>9KHS_4 Ubiquitin (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 5 (A), FASTA

>9KHS_5 E4 ubiquitin-protein ligase UFD2 (chains A)
MTAIEDILQITTDPSDTRGYSLLKSEEVPQGSTLGVDFIDTLLLYQLTENEKLDKPFEYL
NDCFRRNQQQKRITKNKPNAESLHSTFQEIDRLVIGYGVVALQIENFCMNGAFINYITGI
VSNVNSYTDFLSQIIQRAILEGTALDLLNAVFPTLLEYCNKHVSHFDLNESVIYNNVLTI
FELFVTFKPIAEIFTKIDGFFADYSCKPQDFERKTILGPILSLSPIEAAVAIRNYGDNLL
RSKQQTAMIHESLQAEHKVVIDRLFFIVDKLVRGSLNSRTDMISYFAHIANKNHLRRADH
PPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDKIDANYFNNPSLFIDLSGETRLNSD
FKEADAFYDKNRKTADSKPNFISDCFFLTLTYLHYGLGGTLSFEEKMGSEIKALKEEIEK
VKKIAANHDVFARFITAQLSKMEKALKTTESLRFALQGFFAHRSLQLEVFDFICGASTFL
IRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHAPVPFKYYPEFVVEGPVNYSLY
ISKYQTSPIFRNPRLGSFVEFTTMVLRCPELVSNPHLKGKLVQLLSVGAMPLTDNSPGFM
MDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYYKIPSYKN
QLIWQSQNNADFFVRFVARMLNDLTFLLDEGLSNLAEVHNIQNELDNRARGAPPTREEED
KELQTRLASASRQAKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLNYNLESLV
GPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFVRAVD
ILGRKTGLASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVIL
PASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILCFKKQKKEEAKHKAS
E

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 P15731 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1QCQ 2.7 Å, Ubiquitin conjugating enzyme
5AIE 2.8 Å, Not4 ring domain in complex with Ubc4
8J1R 3.52 Å, cryo-EM structures of Ufd4 in complex with Ubc4-Ub
9M7O 4.14 Å, Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation)
9KHT 4.85 Å, cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation)

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