6KC6: HOIP-HOIPIN8 complex

HOIP-HOIPIN8 complex. Determined by X-ray diffraction at 2.12 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 2.12 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,939
Mol. weight: 157.64 kDa
Ligands: ZN, D60
Released: 15 Apr 2020

Explore 6KC6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KC6 contains 55 α-helices and 58 β-strands across 6 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: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	869-870	2	1
β-strand	877-878	2	1
β-strand	887-889	3	2
β-strand	896-898	3	2
α-helix	903	1
β-strand	904	1	2
β-strand	905-906	2	3
β-strand	923-924	2	3
α-helix	931-934	4
α-helix	939-947	9
β-strand	972-973	2	4
β-strand	980	1	5
β-strand	984-985	2	4
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1029	7
α-helix	1030-1034	5
α-helix	1040-1041	2
α-helix	1046-1060	15

Chain C: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	869-870	2	6
β-strand	877-878	2	6
β-strand	887-889	3	7
β-strand	896-898	3	7
α-helix	903	1
β-strand	904	1	7
β-strand	905-906	2	8
β-strand	923-924	2	8
α-helix	931-934	4
α-helix	939-947	9
α-helix	971	1
β-strand	972-973	2	9
α-helix	974-975	2
β-strand	980	1	10
β-strand	984-985	2	9
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1034	12
α-helix	1040-1041	2
α-helix	1046-1060	15
α-helix	1062-1064	3

Chains E and G: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	869-870	2	5
β-strand	877-878	2	5
β-strand	887-889	3	11
β-strand	896-898	3	11
α-helix	903	1
β-strand	904	1	11
β-strand	905-906	2	12
β-strand	923-924	2	12
α-helix	931-934	4
α-helix	939-947	9
β-strand	972-973	2	13
β-strand	980	1	1
β-strand	984-985	2	13
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1034	12
α-helix	1046-1060	15
α-helix	1062	1
α-helix	1064	1

Chain I: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	869-870	2	17
β-strand	877-878	2	17
β-strand	887-889	3	18
β-strand	896-898	3	18
α-helix	903	1
β-strand	904	1	18
β-strand	905-906	2	19
β-strand	923-924	2	19
α-helix	931-934	4
α-helix	939-947	9
β-strand	972-973	2	20
β-strand	984-985	2	20
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1034	12
α-helix	1046-1060	15
α-helix	1062	1
α-helix	1064	1

Chain K: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	869-870	2	21
α-helix	876	1
β-strand	877-878	2	21
β-strand	887-889	3	22
β-strand	896-898	3	22
α-helix	903	1
β-strand	904	1	22
β-strand	905-906	2	23
β-strand	923-924	2	23
α-helix	931-934	4
α-helix	939-947	9
β-strand	972-973	2	24
β-strand	984-985	2	24
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1034	12
α-helix	1046-1060	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF31	A, C, E, G, I, K	protein	225	Homo sapiens	Q96EP0 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>6KC6_1 E3 ubiquitin-protein ligase RNF31 (chains A, C, E, G, I, K)
GPGHMPEYQAQGLAMYLQENGIDCPKCKFSYALARGGCMHFHCTQCRHQFCSGCYNAFYA
KNKCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVMFNTEPPAGARAVPGG
GCRVIEQKEVPNGLRDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELE
TATERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRRRK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	24
D60	2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-propyl]-…	C23 H18 F2 N4 O3	6

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

Primary citation

Molecular bases for HOIPINs-mediated inhibition of LUBAC and innate immune responses. Oikawa, D., Sato, Y., Ohtake, F. et al. Commun Biol (2020) 3:163-163. DOI 10.1038/s42003-020-0882-8 · 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
4LJP 2.15 Å, Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex
6GZY 2.15 Å, HOIP-fragment5 complex

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