7YUJ: HOIL-1L(365-510)

Name: PDB 7YUJ: Crystal structure of HOIL-1L(365-510)
Published: 2023-08-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of HOIL-1L(365-510). Determined by X-ray diffraction at 1.86 Å resolution. Released 30 Aug 2023.

Method: X-ray diffraction
Resolution: 1.86 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,566
Mol. weight: 34.33 kDa
Ligands: ZN
Released: 30 Aug 2023

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

Secondary structure: helices and β-sheets

7YUJ contains 7 α-helices and 22 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: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	368-370	3	1
β-strand	379-381	3	1
β-strand	383	1	2
β-strand	386	1	2
β-strand	388-390	3	3
β-strand	397-399	3	3
β-strand	404	1	3
α-helix	411-421	11
α-helix	426-441	16
β-strand	445-446	2	4
β-strand	453-454	2	4
β-strand	462-464	3	5
β-strand	471-473	3	5
β-strand	478-479	2	5
α-helix	497-499	3

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	362-364	3
β-strand	368-370	3	6
β-strand	379-381	3	6
β-strand	388-390	3	7
β-strand	397-399	3	7
β-strand	404	1	7
α-helix	411-422	12
α-helix	426-441	16
β-strand	444-446	3	8
β-strand	453-455	3	8
β-strand	462-464	3	9
β-strand	471-473	3	9
β-strand	478-479	2	9
α-helix	497-499	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RanBP-type and C3HC4-type zinc finger-containing protein 1	A, B	protein	150	Homo sapiens	Q9BYM8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7YUJ_1 RanBP-type and C3HC4-type zinc finger-containing protein 1 (chains A, B)
GPGSSAFSYHCKTPDCKGWCFFEDDVNEFTCPVCFHVNCLLCKAIHEQMNCKEYQEDLAL
RAQNDVAARQTTEMLKVMLQQGEAMRCPQCQIVVQKKDGCDWIRCTVCHTEICWVTKGPR
WGPGGPGDTSGGCRCRVNGIPCHPSCQNCH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	10

Water and common crystallization additives (PEG) are not listed.

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 Q9BYM8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8K6Q 1.59 Å, Crystal structure of HOIL-1L LTM domain
9EGW 1.78 Å, HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled)
7V8E 1.9 Å, Crystal structure of IpaH1.4 LRR domain bound to HOIL-1L UBL domain.
9EGV 2.0 Å, HOIL-1 RING2 domain bound to ubiquitin
8BVL 2.24 Å, Crystal structure of the IBR-RING2 domain of HOIL-1
7YUI 2.6 Å, Crystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin
4DBG 2.71 Å, Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative
8EAZ 3.08 Å, HOIL-1/E2-Ub/Ub transthiolation complex
2CRC Solution structure of the zf-RanBP domain of the protein HBV associated factor
2LGY Ubiquitin-like domain from HOIL-1

Browse structure collections

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