9M0O | pdb_00009m0o

Crystal structure of OPTN 138-170 in complex with GTP-bound RAB8A1-176 (Q67L)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 
    0.222 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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Literature

Functional and Structural Insights Into Complex Formation Between OPTN Leucine Zipper Domain and RAB8A.

Okatsu, K.Kikuchi, R.Matsuda, N.Fukai, S.Yamano, K.

(2025) Genes Cells 30: e70043-e70043

  • DOI: https://doi.org/10.1111/gtc.70043
  • Primary Citation of Related Structures:  
    9M0O

  • PubMed Abstract: 

    Optineurin (OPTN) is a multifunctional adaptor protein involved in vesicular trafficking and selective autophagy. In this study, we investigated the molecular mechanism by which OPTN regulates these distinct processes through the leucine zipper (LZ) domain. OPTN interacts with the active form of RAB8A and closely related RAB proteins (RAB8B and RAB10). We determined the crystal structure of the OPTN-RAB8A complex at 1.83 Å resolution and elucidated the specific interaction mechanism between these proteins. Structure-guided mutational analysis at the molecular and cellular level suggested that OPTN interacts with RAB8A on two distinct surfaces. RAB8A-interacting surfaces of OPTN include residues that are located apart from the LZ-forming region. Furthermore, the interaction between OPTN and RAB8A was corroborated by cell biological approaches. Although RAB8A/8B/10 were not essential for mitophagy in experiments using their triple knockout cells, the RAB8A-binding residues of OPTN were critical for the recruitment of ATG9A vesicles. Therefore, our results provide molecular insights into the functional role of the LZ domain of OPTN in regulating vesicular trafficking and selective autophagy.


  • Organizational Affiliation
    • Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-8AA [auth D]182Homo sapiensMutation(s): 1 
Gene Names: RAB8AMELRAB8
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61006 (Homo sapiens)
Explore P61006 
Go to UniProtKB:  P61006
PHAROS:  P61006
GTEx:  ENSG00000167461 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61006
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
OptineurinB [auth A]36Homo sapiensMutation(s): 0 
Gene Names: OPTNFIP2GLC1EHIP7HYPLNRP
UniProt & NIH Common Fund Data Resources
Find proteins for Q96CV9 (Homo sapiens)
Explore Q96CV9 
Go to UniProtKB:  Q96CV9
PHAROS:  Q96CV9
GTEx:  ENSG00000123240 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96CV9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
D
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth D],
F [auth D],
H [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
G [auth D]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free:  0.222 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.712α = 90
b = 70.712β = 90
c = 109.25γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19K16068
Japan Society for the Promotion of Science (JSPS)Japan21K15084
Japan Society for the Promotion of Science (JSPS)Japan24H01894
Japan Society for the Promotion of Science (JSPS)Japan18H05501

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release