9EGV: HOIL-1 RING2 domain

Name: PDB 9EGV: HOIL-1 RING2 domain bound to ubiquitin
Published: 2024-12-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

HOIL-1 RING2 domain bound to ubiquitin. Determined by X-ray diffraction at 2.0 Å resolution. Released 11 Dec 2024.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 1,989
Mol. weight: 29.8 kDa
Ligands: ZN
Released: 11 Dec 2024

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

Secondary structure: helices and β-sheets

9EGV contains 8 α-helices and 19 β-strands across 3 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: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	425-440	16
β-strand	445-446	2	1
β-strand	453-457	5	1
β-strand	462-464	3	2
β-strand	471-473	3	2
β-strand	478-479	2	2
α-helix	497-499	3

Chain B: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	432-440	9
β-strand	444-446	3	3
β-strand	453-455	3	3
β-strand	462-464	3	4
β-strand	471-473	3	4
β-strand	478-479	2	4
β-strand	481	1	5
β-strand	492	1	5
α-helix	497-499	3

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	6
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	6
α-helix	57-59	3
β-strand	66-74	9	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RanBP-type and C3HC4-type zinc finger-containing protein 1	A, B	protein	88	Homo sapiens	Q9BYM8 (AlphaFold model)
Polyubiquitin-C	C	protein	88	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9EGV_1 RanBP-type and C3HC4-type zinc finger-containing protein 1 (chains A, B)
GPDVAARQTTEMLKVMLQQGEAMRCPQCQIVVQKKDGADWIRCTVCHTEICWVTKGPRWG
PGGPGDTSGGCRCRVNGIPCHPSCQNCH

Sequence of entity 2 (C), FASTA

>9EGV_2 Polyubiquitin-C (chains C)
MAHHHHHHSAAGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK
QLEDGRTLSDYNIQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Water and common crystallization additives (SO4, CL) are not listed.

Primary citation

The RBR E3 ubiquitin ligase HOIL-1 can ubiquitinate diverse non-protein substrates in vitro. Wang, X.S., Jiou, J., Cerra, A. et al. Life Sci Alliance (2025) 8. DOI 10.26508/lsa.202503243 · 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)
7YUJ 1.86 Å, Crystal structure of HOIL-1L(365-510)
7V8E 1.9 Å, Crystal structure of IpaH1.4 LRR domain bound to HOIL-1L UBL domain.
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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