8Z30: HOIP PUB domain

Name: PDB 8Z30: Crystal structure of HOIP PUB domain in complex with tolfenamic acid complex
Published: 2024-11-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of HOIP PUB domain in complex with tolfenamic acid complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 27 Nov 2024.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,426
Mol. weight: 61.85 kDa
Ligands: TLF, TOE, PE4
Released: 27 Nov 2024

Explore 8Z30 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Z30 contains 30 α-helices and 9 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: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	6-23	18
α-helix	31-38	8
α-helix	44-47	4
α-helix	53-58	6
α-helix	65-87	23
β-strand	97-99	3	1
α-helix	103-107	5
α-helix	109-111	3
α-helix	115-122	8
β-strand	126-128	3	1
β-strand	131-133	3	1
α-helix	143-164	22
α-helix	171-175	5

Chain B: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-23	19
α-helix	31-38	8
α-helix	44-47	4
α-helix	53-58	6
α-helix	65-87	23
β-strand	97-99	3	2
α-helix	103-107	5
α-helix	109-111	3
α-helix	115-122	8
β-strand	126-128	3	2
β-strand	131-133	3	2
α-helix	143-164	22
α-helix	171-175	5

Chain C: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-23	19
α-helix	31-38	8
α-helix	44-47	4
α-helix	53-58	6
α-helix	65-86	22
β-strand	97-99	3	3
α-helix	103-107	5
α-helix	109-111	3
α-helix	115-122	8
β-strand	126-128	3	3
β-strand	131-133	3	3
α-helix	143-164	22
α-helix	171-175	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF31	A, B, C	protein	176	Homo sapiens	Q96EP0 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8Z30_1 E3 ubiquitin-protein ligase RNF31 (chains A, B, C)
EEEERAFLVAREELASALRRDSGQAFSLEQLRPLLASSLPLAARYLQLDAARLVRCNAHG
EPRNYLNTLSTALNILEKYGRNLLSPQRPRYWRGVKFNNPVFRSTVDAVQGGRDVLRLYG
YTEEQPDGLSFPEGQEEPDEHQVATVTLEVLLLRTELSLLLQNTHPRQQALEQLLE

Ligands and cofactors

ID	Name	Formula	Copies
TLF	2-[(3-chloro-2-methylphenyl)amino]benzoic acid	C14 H12 Cl N O2	3
TOE	2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl	C7 H16 O4	1
PE4	2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-etha…	C16 H34 O8	1

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

Primary citation

Repurposing Tolfenamic Acid to Anchor the Uncharacterized Pocket of the PUB Domain for Proteolysis of the Atypical E3 Ligase HOIP. Zhong, F., Zhou, Y., Liu, M. et al. ACS Chem Biol (2024) 19:2469-2476. DOI 10.1021/acschembio.4c00541 · PubMed

Other PDB entries of the same protein (UniProt Q96EP0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KC5 1.54 Å, HOIP-HOIPIN1 complex
4LJO 1.56 Å, Structure of an active ligase (HOIP)/ubiquitin transfer complex
7V8F 1.66 Å, Crystal structure of UBE2L3 bound to HOIP RING1 domain.
4P09 1.7 Å, Crystal structure of HOIP PUB domain
9B0B 1.7 Å, Structure of Optineurin bound to HOIP NZF1 domain
9B12 1.81 Å, Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal…
4OWF 2.0 Å, Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain
4OYK 2.0 Å, Structure of HOIP PUB domain bound to OTULIN PIM
6SC5 2.1 Å, dAb3/HOIP-RBR-Ligand2
6SC8 2.11 Å, dAb3/HOIP-RBR-Ligand4
6KC6 2.12 Å, HOIP-HOIPIN8 complex
4LJP 2.15 Å, Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex

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