8IYA: Complex of SETDB1-derived peptide

Complex of SETDB1-derived peptide bound to UBE2E1. Determined by X-ray diffraction at 2.43 Å resolution. Released 3 Jan 2024.

Method: X-ray diffraction
Resolution: 2.43 Å
Organism: Homo sapiens
Chains: 6
Atoms: 3,913
Mol. weight: 59.96 kDa
Released: 3 Jan 2024

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

Secondary structure: helices and β-sheets

8IYA contains 24 α-helices and 30 β-strands across 6 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	39-61	23
α-helix	63-64	2
β-strand	67-71	5	4
β-strand	78-84	7	4
α-helix	85-86	2
β-strand	95-101	7	4
α-helix	110-111	2
β-strand	112-115	4	4
β-strand	121	1	5
β-strand	124	1	5
β-strand	129	1	4
β-strand	130	1	5
α-helix	133-135	3
α-helix	145-157	13
β-strand	166	1	6
α-helix	167-175	9
α-helix	177-191	15

Chain B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	46-61	16
α-helix	63-64	2
β-strand	67-71	5	1
β-strand	78-84	7	1
α-helix	85-86	2
β-strand	95-101	7	1
α-helix	110-111	2
β-strand	112-115	4	1
β-strand	121	1	2
β-strand	124	1	2
β-strand	129	1	1
β-strand	130	1	2
α-helix	133-135	3
α-helix	145-157	13
β-strand	166	1	3
α-helix	167-175	9
α-helix	177-191	15

Chain C: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	44-61	18
α-helix	63-64	2
β-strand	67-71	5	7
β-strand	78-84	7	7
α-helix	85-86	2
β-strand	95-101	7	7
α-helix	110-111	2
β-strand	112-115	4	7
β-strand	121	1	8
β-strand	124	1	8
β-strand	129	1	7
β-strand	130	1	8
α-helix	133-135	3
α-helix	145-157	13
β-strand	166	1	9
α-helix	167-175	9
α-helix	177-192	16

Chains D, E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	5	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 E1	A, B, C	protein	170	Homo sapiens	P51965 (AlphaFold model)
Histone-lysine N-methyltransferase SETDB1	D, E, F	protein	6	Homo sapiens	Q15047 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8IYA_1 Ubiquitin-conjugating enzyme E2 E1 (chains A, B, C)
MHHHHHHHHLEVLFQGPNSKLLSTSAKRIQKELADITLDPPPNSSAGPKGDNIYEWRSTI
LGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHPNINSQGVICLDILKDNWSPAL
TISKVLLSISSLLTDPNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT

Sequence of entity 2 (D, E, F), FASTA

>8IYA_2 Histone-lysine N-methyltransferase SETDB1 (chains D, E, F)
CEGYES

Primary citation

Structure-guided engineering enables E3 ligase-free and versatile protein ubiquitination via UBE2E1. Wu, X., Du, Y., Liang, L.J. et al. Nat Commun (2024) 15:1266-1266. DOI 10.1038/s41467-024-45635-y · PubMed

Other PDB entries of the same protein (UniProt P51965 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5LBN 1.42 Å, High-resolution crystal structure of the UBC core domain of UBE2E1/UbcH6
3BZH 1.6 Å, Crystal structure of human ubiquitin-conjugating enzyme E2 E1
1XR9 1.79 Å, Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and…
4JJQ 1.95 Å, Crystal structure of usp7-ntd with an e2 enzyme
6FGA 2.82 Å, Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2…

Browse structure collections

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