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- PDB-9m0o: Crystal structure of OPTN 138-170 in complex with GTP-bound RAB8A... -

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Basic information

Entry
Database: PDB / ID: 9m0o
TitleCrystal structure of OPTN 138-170 in complex with GTP-bound RAB8A1-176 (Q67L)
Components
  • Optineurin
  • Ras-related protein Rab-8A
KeywordsPROTEIN BINDING / Membrane Trafficking / autophagy / small GTPase
Function / homology
Function and homology information


neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / type 2 mitophagy / cell death / regulation of protein transport / negative regulation of receptor recycling / Golgi ribbon formation / neurotransmitter receptor transport, endosome to postsynaptic membrane / positive regulation of xenophagy / VxPx cargo-targeting to cilium ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / type 2 mitophagy / cell death / regulation of protein transport / negative regulation of receptor recycling / Golgi ribbon formation / neurotransmitter receptor transport, endosome to postsynaptic membrane / positive regulation of xenophagy / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / protein localization to Golgi apparatus / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / Golgi to plasma membrane protein transport / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / ciliary membrane / K63-linked polyubiquitin modification-dependent protein binding / ciliary base / Golgi organization / exocytosis / cilium assembly / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / phagocytic vesicle / negative regulation of canonical NF-kappaB signal transduction / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / positive regulation of autophagy / centriole / TICAM1-dependent activation of IRF3/IRF7 / axonogenesis / Anchoring of the basal body to the plasma membrane / autophagosome / protein tyrosine kinase binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / trans-Golgi network membrane / PINK1-PRKN Mediated Mitophagy / small monomeric GTPase / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Regulation of TNFR1 signaling / trans-Golgi network / regulation of long-term neuronal synaptic plasticity / small GTPase binding / autophagy / centriolar satellite / phagocytic vesicle membrane / recycling endosome membrane / cellular response to insulin stimulus / synaptic vesicle / GDP binding / Regulation of PLK1 Activity at G2/M Transition / actin cytoskeleton / midbody / protein-macromolecule adaptor activity / defense response to Gram-negative bacterium / lysosome / endosome / endosome membrane / regulation of autophagy / cilium / ciliary basal body / Golgi membrane / innate immune response / neuronal cell body / GTPase activity / dendrite / centrosome / GTP binding / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / signal transduction / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / : / ARF-like small GTPases; ARF, ADP-ribosylation factor ...NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-8A / Optineurin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsOkatsu, K. / Fukai, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K16068 Japan
Japan Society for the Promotion of Science (JSPS)21K15084 Japan
Japan Society for the Promotion of Science (JSPS)24H01894 Japan
Japan Society for the Promotion of Science (JSPS)18H05501 Japan
CitationJournal: Genes Cells / Year: 2025
Title: Functional and Structural Insights Into Complex Formation Between OPTN Leucine Zipper Domain and RAB8A.
Authors: Okatsu, K. / Kikuchi, R. / Matsuda, N. / Fukai, S. / Yamano, K.
History
DepositionFeb 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Ras-related protein Rab-8A
A: Optineurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0158
Polymers25,1322
Non-polymers8836
Water3,747208
1
D: Ras-related protein Rab-8A
A: Optineurin
hetero molecules

D: Ras-related protein Rab-8A
A: Optineurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,02916
Polymers50,2644
Non-polymers1,76612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5560 Å2
ΔGint-28 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.712, 70.712, 109.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules DA

#1: Protein Ras-related protein Rab-8A / Oncogene c-mel


Mass: 21095.283 Da / Num. of mol.: 1 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Production host: Escherichia coli (E. coli) / References: UniProt: P61006, small monomeric GTPase
#2: Protein/peptide Optineurin / E3-14.7K-interacting protein / FIP-2 / Huntingtin yeast partner L / Huntingtin-interacting protein ...E3-14.7K-interacting protein / FIP-2 / Huntingtin yeast partner L / Huntingtin-interacting protein 7 / HIP-7 / Huntingtin-interacting protein L / NEMO-related protein / Optic neuropathy-inducing protein / Transcription factor IIIA-interacting protein / TFIIIA-IntP


Mass: 4036.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 138-170 / Source: (gene. exp.) Homo sapiens (human) / Gene: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96CV9

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Non-polymers , 5 types, 214 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Imidazole pH 6.5, 0.5 M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 25176 / % possible obs: 100 % / Redundancy: 25.9 % / Biso Wilson estimate: 27.11 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.242 / Net I/σ(I): 18.46
Reflection shellResolution: 1.83→1.9 Å / Num. unique obs: 25125 / CC1/2: 0.956

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→45.47 Å / SU ML: 0.2147 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 1259 5 %
Rwork0.1895 23917 -
obs0.1911 25176 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.42 Å2
Refinement stepCycle: LAST / Resolution: 1.83→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 55 208 1978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721790
X-RAY DIFFRACTIONf_angle_d0.90442401
X-RAY DIFFRACTIONf_chiral_restr0.0557267
X-RAY DIFFRACTIONf_plane_restr0.0058297
X-RAY DIFFRACTIONf_dihedral_angle_d21.9195250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.90.34851360.33562595X-RAY DIFFRACTION99.74
1.9-1.990.30581370.25662592X-RAY DIFFRACTION99.82
1.99-2.090.27791380.23632615X-RAY DIFFRACTION99.78
2.09-2.220.22591380.21022613X-RAY DIFFRACTION99.89
2.22-2.40.22221380.1842630X-RAY DIFFRACTION99.93
2.4-2.640.23851400.19442651X-RAY DIFFRACTION99.96
2.64-3.020.21261400.18382655X-RAY DIFFRACTION99.96
3.02-3.80.21121420.16962708X-RAY DIFFRACTION100
3.8-45.470.19311500.1692858X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 16.3448816288 Å / Origin y: 2.80560843549 Å / Origin z: 15.4182396181 Å
111213212223313233
T0.19568295371 Å2-0.0751443627919 Å20.0230765902213 Å2-0.278617982639 Å2-0.0152866138296 Å2--0.157641968649 Å2
L2.05090124689 °2-0.671888725831 °20.483053759194 °2-2.25909107372 °2-0.801877065979 °2--2.54362024955 °2
S-0.140993307664 Å °-0.2293907671 Å °-0.0810060776917 Å °0.0155855538108 Å °0.201751950404 Å °0.199312412819 Å °0.192270899799 Å °-0.435247445405 Å °-0.00156597713325 Å °
Refinement TLS groupSelection details: all

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