8BVL: IBR-RING2 domain of HOIL-1

Crystal structure of the IBR-RING2 domain of HOIL-1. Determined by X-ray diffraction at 2.24 Å resolution. Released 18 Jan 2023.

Method: X-ray diffraction
Resolution: 2.24 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,340
Mol. weight: 33.33 kDa
Ligands: ZN
Released: 18 Jan 2023

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

Secondary structure: helices and β-sheets

8BVL contains 8 α-helices and 24 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: 4 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
α-helix	396	1
β-strand	397-399	3	3
β-strand	404	1	3
α-helix	411-420	10
α-helix	426-440	15
β-strand	444-446	3	4
β-strand	453-455	3	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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	368-370	3	6
β-strand	379-381	3	6
β-strand	383	1	7
β-strand	386	1	7
β-strand	388-390	3	8
α-helix	396	1
β-strand	397-399	3	8
β-strand	404	1	8
α-helix	411-419	9
α-helix	426-440	15
β-strand	444-446	3	9
β-strand	453-455	3	9
β-strand	462-464	3	10
β-strand	471-473	3	10
β-strand	478-479	2	10
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	145	Homo sapiens	Q9BYM8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8BVL_1 RanBP-type and C3HC4-type zinc finger-containing protein 1 (chains A, B)
GPSYHCKTPDCKGWCFFEDDVNEFTCPVCFHVNCLLCKAIHEQMNCKEYQEDLALRAQND
VAARQTTEMLKVMLQQGEAMRCPQCQIVVQKKDGCDWIRCTVCHTEICWVTKGPRWGPGG
PGDTSGGCRCRVNGIPCHPSCQNCH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	10

Primary citation

Structural basis for ubiquitylation by HOIL-1. Wu, Q., Koliopoulos, M.G., Rittinger, K. et al. Front Mol Biosci (2022) 9:1098144-1098144. DOI 10.3389/fmolb.2022.1098144 · 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.
9EGV 2.0 Å, HOIL-1 RING2 domain bound to ubiquitin
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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