9B12: Optineurin

Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1. Determined by X-ray diffraction at 1.81 Å resolution. Released 31 Jul 2024.

Method: X-ray diffraction
Resolution: 1.81 Å
Organism: Homo sapiens
Chains: 10
Atoms: 6,089
Mol. weight: 93.47 kDa
Ligands: ZN
Released: 31 Jul 2024

Explore 9B12 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B12 contains 15 α-helices and 41 β-strands across 10 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: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-44	4	1
β-strand	45	1	2
β-strand	48	1	2
β-strand	66-71	6	1
β-strand	78-83	6	3
β-strand	88-92	5	3
β-strand	98	1	4
α-helix	99-110	12
α-helix	114-116	3
β-strand	117-121	5	3
β-strand	124-125	2	3
β-strand	131	1	4
α-helix	132-135	4
β-strand	142-147	6	3

Chain B: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	5
α-helix	23-29	7
α-helix	31-34	4
α-helix	38-40	3
β-strand	41-43	3	6
β-strand	45	1	7
β-strand	48	1	7
β-strand	66-68	3	5
β-strand	69-71	3	6
β-strand	78-83	6	8
β-strand	88-92	5	8
β-strand	98	1	9
α-helix	99-110	12
α-helix	114-116	3
β-strand	117-121	5	8
β-strand	124-125	2	8
β-strand	131	1	9
β-strand	142-147	6	8

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	420-504	85

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	422-506	85

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	419-458	40
α-helix	460-504	45

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	419-504	86

Chains G, H, I and J: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	354-355	2	10
β-strand	362-363	2	10
β-strand	369	1	11
β-strand	376	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Optineurin	C, D, E, F	protein	96	Homo sapiens	Q96CV9 (AlphaFold model)
Ubiquitin	A, B	protein	152	Homo sapiens	P0CG47 (AlphaFold model)
E3 ubiquitin-protein ligase RNF31	G, H, I, J	protein	30	Homo sapiens	Q96EP0 (AlphaFold model)

Sequence of entity 1 (C, D, E, F), FASTA

>9B12_1 Optineurin (chains C, D, E, F)
GPDRAVLKELSEKLELAEKALASKQLQMDEMKQTIAKQEEDLETMTILRAQMEVYCSDFH
AERAAREKIHEEKEQLALQLAVLLKENDAFEDGGRQ

Sequence of entity 2 (A, B), FASTA

>9B12_2 Ubiquitin (chains A, B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI
FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Sequence of entity 3 (G, H, I, J), FASTA

>9B12_3 E3 ubiquitin-protein ligase RNF31 (chains G, H, I, J)
ARGRWACQSCTFENEAAAVLCSICERPRLA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (PG4, CL, EPE, PGE) are not listed.

Primary citation

Linkage and substrate specificity conferred by NZF ubiquitin binding domains. Michel, M.A., Scutts, S., Komander, D. To be published.

Other PDB entries of the same protein (UniProt Q96CV9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VTV 1.7 Å, Crystal structure of Optineurin LIR-fused human LC3B_2-119
9B0B 1.7 Å, Structure of Optineurin bound to HOIP NZF1 domain
9M0O 1.83 Å, Crystal structure of OPTN 138-170 in complex with GTP-bound RAB8A1-176 (Q67L)
9IKQ 1.93 Å, Crystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L)
7CZM 2.0 Å, Crystal structure of FIP200 Claw/p-OPtineurin LIR complex
5EOF 2.05 Å, Crystal structure of OPTN NTD and TBK1 CTD complex
9B0Z 2.41 Å, Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal…
5EOA 2.5 Å, Crystal structure of OPTN E50K mutant and TBK1 complex
3VTW 2.52 Å, Crystal structure of T7-tagged Optineurin LIR-fused human LC3B_2-119
5B83 2.69 Å, Crystal structure of Optineurin UBAN in complex with linear ubiquitin
2LO4 NMR Solution Structure of Optineurin Zinc-finger Domain
2LUE LC3B OPTN-LIR Ptot complex structure

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