7YUI: HOIL-1L(195-423)

Crystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin. Determined by X-ray diffraction at 2.6 Å resolution. Released 30 Aug 2023.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,352
Mol. weight: 61.72 kDa
Ligands: ZN
Released: 30 Aug 2023

Explore 7YUI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YUI contains 27 α-helices and 46 β-strands across 2 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: 15 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	1
β-strand	12-17	6	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
β-strand	66-71	6	1
β-strand	77-83	7	3
β-strand	88-93	6	3
β-strand	98	1	4
α-helix	99-110	12
α-helix	114-116	3
β-strand	117-121	5	3
β-strand	124-125	2	3
α-helix	126-127	2
β-strand	131	1	4
β-strand	142-147	6	3
β-strand	154-158	5	5
α-helix	163	1
β-strand	164-168	5	5
β-strand	174	1	6
α-helix	175-186	12
α-helix	190-192	3
β-strand	193-197	5	5
β-strand	200-201	2	5
α-helix	202-203	2
β-strand	207	1	6
α-helix	209-211	3
β-strand	217-223	7	5
β-strand	229-235	7	7
β-strand	240-245	6	7
β-strand	250	1	8
α-helix	251-262	12
α-helix	266-268	3
β-strand	269-273	5	7
β-strand	276-277	2	7
α-helix	278-279	2
β-strand	283	1	8
β-strand	294-299	6	7
α-helix	300-302	3

Chain B: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	197-198	2	9
β-strand	205-206	2	9
β-strand	212	1	10
α-helix	218	1
β-strand	219	1	10
α-helix	220-221	2
α-helix	234-267	34
α-helix	268-270	3
β-strand	274-275	2	11
β-strand	280-281	2	12
β-strand	288-289	2	12
β-strand	295-296	2	11
β-strand	303-304	2	11
α-helix	306-314	9
α-helix	321	1
β-strand	322	1	13
α-helix	323	1
β-strand	326	1	14
β-strand	331	1	14
β-strand	335	1	13
α-helix	338-344	7
α-helix	347-364	18
β-strand	368-370	3	15
β-strand	379-381	3	15
α-helix	382-383	2
β-strand	388-390	3	16
α-helix	396	1
β-strand	397-399	3	16
β-strand	404	1	16
α-helix	411-421	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyubiquitin-C	A	protein	308	Homo sapiens	P0CG48 (AlphaFold model)
RanBP-type and C3HC4-type zinc finger-containing protein 1	B	protein	234	Homo sapiens	Q9BYM8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7YUI_1 Polyubiquitin-C (chains A)
GPGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIE
NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL
TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH
LVLRLRGG

Sequence of entity 2 (B), FASTA

>7YUI_2 RanBP-type and C3HC4-type zinc finger-containing protein 1 (chains B)
GSEFVGWQCPGCTFINKPTRPGCEMCCRARPEAYQVPASYQPDEEERARLAGEEEALRQY
QQRKQQQQEGNYLQHVQLDQRSLVLNTEPAECPVCYSVLAPGEAVVLRECLHTFCRECLQ
GTIRNSQEAEVSCPFIDNTYSCSGKLLEREIKALLTPEDYQRFLDLGISIAENRSAFSYH
CKTPDCKGWCFFEDDVNEFTCPVCFHVNCLLCKAIHEQMNCKEYQEDLALRAQN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	5

Primary citation

Mechanistic insights into the enzymatic activity of E3 ligase HOIL-1L and its regulation by the linear ubiquitin chain binding. Xu, X., Wang, Y., Zhang, Y. et al. Sci Adv (2023) 9:eadi4599-eadi4599. DOI 10.1126/sciadv.adi4599 · 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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