4DBG: HOIL-1L-UBL

Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative. Determined by X-ray diffraction at 2.71 Å resolution. Released 4 Apr 2012.

Method: X-ray diffraction
Resolution: 2.71 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,859
Mol. weight: 30.23 kDa
Released: 4 Apr 2012

Explore 4DBG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DBG contains 16 α-helices and 7 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, 7 β-strands

Element	Residues	Length	Sheet
β-strand	55-63	9	1
β-strand	69-75	7	1
β-strand	80	1	2
α-helix	81-92	12
α-helix	96-98	3
β-strand	99-103	5	1
β-strand	106-108	3	1
α-helix	109	1
β-strand	113	1	2
α-helix	115-117	3
β-strand	125-130	6	1

Chain B: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	483-493	11
α-helix	505-515	11
α-helix	521-527	7
α-helix	531-542	12
α-helix	544-546	3
α-helix	548-550	3
α-helix	551-560	10
α-helix	565-585	21
α-helix	590-592	3
α-helix	594-600	7
α-helix	605-616	12
α-helix	618-625	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RanBP-type and C3HC4-type zinc finger-containing protein 1	A	protein	105	Homo sapiens	Q9BYM8 (AlphaFold model)
RING finger protein 31	B	protein	162	Homo sapiens	Q96EP0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DBG_1 RanBP-type and C3HC4-type zinc finger-containing protein 1 (chains A)
GSHMQRVPLSVQLKPEVSPTQDIRLWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDY
GFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLLSARNTS

Sequence of entity 2 (B), FASTA

>4DBG_2 RING finger protein 31 (chains B)
GPLGSRQDKMREEGLQLVSMIREGEAAGACPEEIFSALQYSGTEVPLQWLRSELPYVLEM
VAELAGQQDPGLGAFSCQEARRAWLDRHGNLDEAVEECVRTRRRKVQELQSLGFGPEEGS
LQALFQHGGDVSRALTELQRQRLEPFRQRLWDSGPEPTPSWD

Primary citation

A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex. Yagi, H., Ishimoto, K., Hiromoto, T. et al. EMBO Rep (2012) 13:462-468. DOI 10.1038/embor.2012.24 · 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
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
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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