9EYH: Ubiquitin-conjugating enzyme E2 6

Ubiquitin conjugating enzyme Ubc6 UBC domain with isopeptide-linked ubiquitin. Determined by X-ray diffraction at 2.6 Å resolution. Released 20 Nov 2024.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 3,945
Mol. weight: 57.88 kDa
Released: 20 Nov 2024

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

Secondary structure: helices and β-sheets

9EYH contains 21 α-helices and 28 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-19	16
α-helix	21-22	2
β-strand	25-30	6	1
β-strand	33-42	10	1
α-helix	43-44	2
β-strand	53-59	7	1
α-helix	68-69	2
β-strand	70-73	4	1
β-strand	80	1	2
α-helix	104-116	13
β-strand	124	1	2
α-helix	129-145	17
α-helix	148-153	6
α-helix	155-168	14

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-19	16
α-helix	21-22	2
β-strand	25-30	6	3
β-strand	33-42	10	3
α-helix	43-44	2
β-strand	53-59	7	3
α-helix	68-69	2
β-strand	70-73	4	3
β-strand	80	1	4
β-strand	89	1	5
α-helix	104-116	13
β-strand	124	1	4
α-helix	129-145	17
α-helix	148-153	6
α-helix	155-169	15

Chain C: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
β-strand	12-16	5	6
β-strand	22	1	7
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-45	5	6
β-strand	48-49	2	6
β-strand	55	1	7
β-strand	66-71	6	6

Chain D000: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	12-15	4	8
β-strand	22	1	9
α-helix	23-33	11
α-helix	38-40	3
β-strand	42-44	3	8
β-strand	49	1	8
β-strand	55	1	9
α-helix	57-59	3
β-strand	66-70	5	8
β-strand	74	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 6	A, B	protein	178	Saccharomyces cerevisiae	P33296 (AlphaFold model)
Ubiquitin-40S ribosomal protein S31	C, D000	protein	76	Saccharomyces cerevisiae	P05759 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9EYH_1 Ubiquitin-conjugating enzyme E2 6 (chains A, B)
MATKQAHKRLTKEYKLMVENPPPYILARPNEDNILEWHYIITGPADTPYKGGQYHGTLTF
PSDYPYKPPAIRMITPNGRFKPNTRLKLSMSDYHPDTWNPGWSVSTILNGLLSFMTSDEA
TTGSITTSDHQKKTLARNSISYNTFQNVRFKLIFPEVVQENVETLEKRKLDELPETGG

Sequence of entity 2 (C, D000), FASTA

>9EYH_2 Ubiquitin-40S ribosomal protein S31 (chains C, D000)
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes. Swarnkar, A., Leidner, F., Rout, A.K. et al. EMBO J (2024) 43:6705-6739. DOI 10.1038/s44318-024-00301-3 · PubMed

Other PDB entries of the same protein (UniProt P33296 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EWP 1.21 Å, Crystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 UBC domain
9EN5 1.33 Å, Crystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 UBC domain

Browse structure collections

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