9IKQ: OPTN LZD

Crystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L). Determined by X-ray diffraction at 1.93 Å resolution. Released 25 Dec 2024.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,021
Mol. weight: 52.02 kDa
Ligands: MG, GTP
Released: 25 Dec 2024

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

Secondary structure: helices and β-sheets

9IKQ contains 18 α-helices and 17 β-strands across 4 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	1
α-helix	21-30	10
β-strand	43-52	10	1
β-strand	55-64	10	1
α-helix	68-70	3
α-helix	71-75	5
β-strand	83-89	7	1
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	1
α-helix	126-128	3
α-helix	133-143	11
β-strand	146-149	4	1
β-strand	151	1	2
β-strand	156	1	2
α-helix	158-175	18

Chain B: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	3
α-helix	21-30	10
β-strand	43-52	10	3
β-strand	55-64	10	3
α-helix	68-70	3
α-helix	71-75	5
β-strand	83-89	7	3
β-strand	92	1	3
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	3
α-helix	133-143	11
β-strand	146-149	4	3
β-strand	151	1	4
β-strand	156	1	4
α-helix	158-178	21

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	136-139	4
α-helix	140-168	29

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	140-168	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-8A	A, B	protein	181	Homo sapiens	P61006 (AlphaFold model)
Optineurin	C, D	protein	38	Homo sapiens	Q96CV9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9IKQ_1 Ras-related protein Rab-8A (chains A, B)
MAKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQ
IWDTAGLERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILG
NKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKKLEGN
S

Sequence of entity 2 (C, D), FASTA

>9IKQ_2 Optineurin (chains C, D)
RAEAEQEKDQLRTQVVRLQAEKADLLGIVSELQLKLNS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

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

Primary citation

Molecular Basis of the Recognition of the Active Rab8a by Optineurin. Zhang, J., Liu, L., Li, M. et al. J Mol Biol (2024) 436:168811-168811. DOI 10.1016/j.jmb.2024.168811 · PubMed

Other PDB entries of the same protein (UniProt P61006 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LHW 1.55 Å, Crystal structure of Rab8 in its active GppNHp-bound form
6SQ2 1.68 Å, Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab…
6WHE 1.73 Å, Structure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state
6RIR 1.77 Å, Crystal structure of phosphorylated Rab8a in complex with the Rab-binding domain of RILPL2
9M0O 1.83 Å, Crystal structure of OPTN 138-170 in complex with GTP-bound RAB8A1-176 (Q67L)
7LWB 1.9 Å, Crystal Structure of phospho-Rab8a with the RH2 domain (117-165) of RILPL2
6ZSI 1.91 Å, The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members.
4LHV 1.95 Å, Crystal structure of Rab8 in its inactive GDP-bound form
3QBT 2.0 Å, Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp
6ZSJ 2.0 Å, The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members.
6YX5 2.14 Å, Structure of DrrA from Legionella pneumophilia in complex with human Rab8a
7BWT 2.3 Å, SopD-Rab8 complex structure

Browse structure collections

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