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- PDB-9ikq: Crystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L) -

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Basic information

Entry
Database: PDB / ID: 9ikq
TitleCrystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L)
Components
  • Optineurin
  • Ras-related protein Rab-8A
KeywordsPROTEIN BINDING / Rab8a / Optineurin
Function / homology
Function and homology information


neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / type 2 mitophagy / cell death / vesicle-mediated transport in synapse / negative regulation of receptor recycling / Golgi ribbon formation / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to Golgi apparatus ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / type 2 mitophagy / cell death / vesicle-mediated transport in synapse / negative regulation of receptor recycling / Golgi ribbon formation / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to Golgi apparatus / positive regulation of xenophagy / VxPx cargo-targeting to cilium / myosin V binding / RAB geranylgeranylation / Golgi to plasma membrane protein transport / trans-Golgi network transport vesicle / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / non-motile cilium / vesicle docking involved in exocytosis / regulation of canonical NF-kappaB signal transduction / TBC/RABGAPs / 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 / positive regulation of autophagy / centriole / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1-dependent activation of IRF3/IRF7 / Anchoring of the basal body to the plasma membrane / axonogenesis / autophagosome / protein tyrosine kinase binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / small monomeric GTPase / trans-Golgi network membrane / protein localization to plasma membrane / PINK1-PRKN Mediated Mitophagy / TNFR1-induced NF-kappa-B signaling pathway / 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 / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / actin cytoskeleton / midbody / protein-macromolecule adaptor activity / defense response to Gram-negative bacterium / lysosome / endosome / regulation of autophagy / endosome membrane / ciliary basal body / cilium / Golgi membrane / innate immune response / neuronal cell body / GTPase activity / centrosome / dendrite / 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 / cytosol / cytoplasm
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 Rab1 family 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
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-8A / Optineurin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhang, J. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21822705 China
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Molecular Basis of the Recognition of the Active Rab8a by Optineurin.
Authors: Zhang, J. / Liu, L. / Li, M. / Liu, H. / Gong, X. / Tang, Y. / Zhang, Y. / Zhou, X. / Lin, Z. / Guo, H. / Pan, L.
History
DepositionJun 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,02318
Polymers50,1884
Non-polymers1,83614
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.218, 69.432, 110.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 20766.906 Da / Num. of mol.: 2 / 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: 4326.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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, 421 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M BIS-TRIS pH 6.5, 16% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98655 Å / Relative weight: 1
ReflectionResolution: 1.93→57.4 Å / Num. obs: 39526 / % possible obs: 99.8 % / Redundancy: 12.3 % / Biso Wilson estimate: 31.25 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 13.5
Reflection shellResolution: 1.93→1.96 Å / Rmerge(I) obs: 0.899 / Num. unique obs: 1833

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LHW

4lhw


Resolution: 1.93→43.19 Å / SU ML: 0.2387 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.653
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2182 1816 4.86 %
Rwork0.1743 35583 -
obs0.1763 37399 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.25 Å2
Refinement stepCycle: LAST / Resolution: 1.93→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 114 407 3927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873658
X-RAY DIFFRACTIONf_angle_d1.0524915
X-RAY DIFFRACTIONf_chiral_restr0.0565544
X-RAY DIFFRACTIONf_plane_restr0.0042617
X-RAY DIFFRACTIONf_dihedral_angle_d14.2635505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.30121560.26992556X-RAY DIFFRACTION91.31
1.98-2.040.2681190.23832835X-RAY DIFFRACTION97.91
2.04-2.110.24951190.21232796X-RAY DIFFRACTION97.33
2.11-2.180.23221440.19712711X-RAY DIFFRACTION95.74
2.18-2.270.24461400.19442785X-RAY DIFFRACTION97.21
2.27-2.370.23591610.17972767X-RAY DIFFRACTION96.83
2.37-2.50.23221730.17792721X-RAY DIFFRACTION95.92
2.5-2.650.26781310.18332712X-RAY DIFFRACTION94.39
2.65-2.860.21461190.182786X-RAY DIFFRACTION95.37
2.86-3.140.23731140.17422771X-RAY DIFFRACTION94.65
3.15-3.60.21431650.16472693X-RAY DIFFRACTION92.67
3.6-4.530.16781200.13932742X-RAY DIFFRACTION92.26
4.54-43.190.19251550.15982708X-RAY DIFFRACTION88.2
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.482555876420.2924942691350.6455363872612.5932154670.6274101692772.85852895880.01085252025730.1140552352080.350061624878-0.0888664111171-0.04056497232780.0597588507653-0.414966555745-0.00252223392190.04213312625790.2093506268350.001663846818790.01549606679250.1437572714330.01662907084130.141577015324-18.438366200822.1184682702-28.7445751027
24.564558651540.7737519978380.341907514073.942883731430.2288910516173.555985328310.230673296883-0.2643174339250.3170867340680.263373404367-0.0258164595355-0.833859218159-0.605964156762-0.1038895622110.06210646826630.2763622208510.0002599863577920.01779794370330.1351996046750.01406606598870.281185817698-12.227464238327.7857824668-27.1311158295
36.202059992731.837745164032.443013113025.326458884472.246241673126.53128862908-0.0724621895291-0.175424141910.2836596366780.004241699199480.0849091960417-0.552163480964-0.7160089043460.262443024218-0.01590024376150.237598713005-0.0331041323580.004152724074720.2140579366550.006007598396710.18683986793-8.497556754126.7880511759-24.9495666476
43.318728308970.165451591292-1.533979183262.739731681250.0118501612283.56884363390.0197951971848-0.05811889294060.0225048479227-0.103293255169-0.0790847470463-0.227485494515-0.01801626442490.1722889883030.06500538275750.1497867093670.0219510242629-0.01763809720320.133687724370.0200919526080.137256554818-13.978868199510.9770816494-29.3870629694
51.7850128116-0.240781542464-1.807630385684.07154676342-0.1357208723743.89712548508-0.0550122531698-0.191439865628-0.5142366742090.186060322639-0.06604763399160.07664420359240.2125762291550.1366513815880.1249233548390.2068551718520.03101015041760.008052896830160.180812935585-0.003882266565360.171319104346-15.19486087253.67478858394-23.4752354533
60.768048388321-1.19328354892-0.8092876034752.82234443746-0.01393096203473.39863241676-0.0522682063348-0.239716762311-0.005584319516280.220227088989-0.01611223163350.105541774214-0.120488799708-0.1580061037330.05632859048620.200903608282-0.005078046944250.004687521251510.1756448555340.006868079685870.140631634812-22.564193930612.4450355102-18.9084017189
72.20231064005-0.2622278287680.645331598493.05917328798-1.974530124544.30070379551-0.112285494318-0.523462175389-0.0977689313290.5666811238940.04727196198310.0849015706894-0.247902188369-0.08531149794620.04351987692710.2586860746470.01654057072040.01772311109150.28106793342-0.01871099666320.146229724152-20.50302164956.38440999481-10.8067876045
82.54266601748-0.3303195128490.314725820142.75982700277-0.1844394366861.46234327739-0.017669112773-0.2797562612610.2028089672470.371613225668-0.0139303943221-0.245478079674-0.245351840070.1960214882570.02902615306630.311604490407-0.0457415814496-0.01402566895810.251243582467-0.03637156188880.183451675313-12.961109405821.3593181-15.7523302884
93.497703965661.18759243686-0.3848897511789.51129039444-2.98783906777.648265266190.6143805978280.795047944305-2.94501402771-0.391036018522-0.2305264475190.9639692355520.783302554258-1.17558906207-0.4999945149770.4603342368850.0897394366570.01679388553670.8327754584830.03505219611081.24812709228-33.739678969335.8227062108-38.0332056556
108.78476869788-3.47302514356-1.224591260136.62630268381-0.4179476770263.424541661460.272987669743-0.2756778791140.45999857750.14070257652-0.0531779544505-0.0100941975722-0.3077873736440.0670292162834-0.1429722672150.265387298862-0.04630835805890.03807195540850.1834832883890.04125254109190.156738472434-8.8275790756529.9502907775-38.8919925067
116.09415614969-2.584123690770.2058666885476.22931996217-1.112641038734.726975230990.2085419091940.3179988589270.263090542263-0.12331117933-0.0880766910310.237976265498-0.305677978102-0.298793847572-0.0799783704210.18777218364-0.01658352574650.0886569366080.2238985166470.04383343607160.182320046846-13.278675720927.1026312649-44.0283428596
122.88513125843-0.05073278925970.3403069094243.38458364230.5533837608583.19440761072-0.0240302236741-0.0315811116373-0.06601628087240.129298390020.009214020131370.423119038996-0.145817639976-0.470562674580.01092403335310.1246453491520.01289984941330.0181641767530.197953997320.0149008628440.174716834874-5.7705882340335.2086380417-53.7078531536
134.840285533740.4009350452870.5018796753414.659106760820.9270610420795.51820327559-0.1198425281040.299696574984-0.483087408161-0.0749924059090.07733245776860.4575545772770.0583482726591-0.5768805305780.007995527543470.169452074059-0.02995943716040.01498401789470.2349256444420.02385877222260.224242319002-10.773226046427.3798628137-56.7017900155
142.581756744690.239499590470.07670531644831.600685627360.03533368143933.81713698948-0.0455749534342-0.125984163346-0.1415599444540.04463080681090.0346352605196-0.08874246314920.1729578723380.1271827184430.0108512540530.1467663822130.03765760710520.01766226185490.1667392515670.003099187776130.1816636287545.7400342601831.9128564637-53.1420032976
154.86806253624-1.48893324668-0.7733896610277.92649331448-0.04899290085483.66009384637-0.02576207199920.0929357455199-0.2563039435260.0979640910889-0.0200396195071-0.1708975141960.197446669210.1261878242210.0396849521550.1563645728960.02795960530050.03552875810440.172065689816-0.001445168547610.0973074325419.1012741129431.1569085514-60.804370204
164.01912952225-1.32960155217-1.754787739882.704616279091.381365729724.302134925030.2155024988710.3774563859280.447959243234-0.374443974554-0.16770725319-0.196094670008-0.566254011393-0.068267634502-0.1387253440950.235537023392-0.01497335188110.0004137937511740.2166850693180.06305580063310.1876571510447.0964740584544.2586472934-67.7071475383
172.365776178440.143926758208-0.6354330343722.750536275170.1975289827032.12792418418-0.07936525598610.407697375547-0.151674163554-0.1023045346730.06089267232820.2018229138140.232286509372-0.3549961522110.04373383429940.170228427168-0.0134883766835-0.01739517518520.302286636385-0.01117783497220.152005365133-5.2756825118730.1210269632-67.0927291335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 64 )
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 92 )
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 109 )
6X-RAY DIFFRACTION6chain 'A' and (resid 110 through 132 )
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 143 )
8X-RAY DIFFRACTION8chain 'A' and (resid 144 through 177 )
9X-RAY DIFFRACTION9chain 'C' and (resid 134 through 139 )
10X-RAY DIFFRACTION10chain 'C' and (resid 140 through 170 )
11X-RAY DIFFRACTION11chain 'D' and (resid 136 through 170 )
12X-RAY DIFFRACTION12chain 'B' and (resid 3 through 42 )
13X-RAY DIFFRACTION13chain 'B' and (resid 43 through 64 )
14X-RAY DIFFRACTION14chain 'B' and (resid 65 through 92 )
15X-RAY DIFFRACTION15chain 'B' and (resid 93 through 121 )
16X-RAY DIFFRACTION16chain 'B' and (resid 122 through 143 )
17X-RAY DIFFRACTION17chain 'B' and (resid 144 through 179 )

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