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- PDB-9odx: Structure of Unc119B in complex with N-acetyl-S-geranylgeranyl-L-... -

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Basic information

Entry
Database: PDB / ID: 9odx
TitleStructure of Unc119B in complex with N-acetyl-S-geranylgeranyl-L-Cysteine
ComponentsProtein unc-119 homolog B
KeywordsLIPID BINDING PROTEIN / Unc119 / TRANSPORT PROTEIN
Function / homology
Function and homology information


Trafficking of myristoylated proteins to the cilium / ciliary transition zone / lipoprotein transport / cilium assembly / lipid binding
Similarity search - Function
: / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Immunoglobulin E-set
Similarity search - Domain/homology
: / Protein unc-119 homolog B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSrivastava, D. / Sebag, J.A. / Artemyev, N.O.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Mol Metab / Year: 2025
Title: Inhibition of Unc119b improves insulin sensitivity through potentiation of Rac1 activation in skeletal muscle and brown adipose tissue.
Authors: Mittal, A. / Buscaglia, P. / Srivastava, D. / Artemyev, N.O. / Sebag, J.A.
History
DepositionApr 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein unc-119 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5043
Polymers25,9721
Non-polymers5322
Water2,792155
1
A: Protein unc-119 homolog B
hetero molecules

A: Protein unc-119 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0086
Polymers51,9442
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4970 Å2
ΔGint-40 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.670, 62.641, 51.872
Angle α, β, γ (deg.)90.000, 117.743, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Protein unc-119 homolog B


Mass: 25972.070 Da / Num. of mol.: 1 / Fragment: residues 54-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Unc119b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C4B4
#2: Chemical ChemComp-A1CA2 / N-acetyl-S-geranylgeranyl-L-cysteine / N-acetyl-S-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-L-cysteine


Mass: 435.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H41NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M bis-tris propane/tris, 1.5-2.2 M Ammonium sulphate, pH 5.5-8.5
PH range: 5.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→47.09 Å / Num. obs: 40180 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 15.4
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1983 / CC1/2: 0.67 / Rpim(I) all: 0.42 / Rrim(I) all: 0.803 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→47.09 Å / SU ML: 0.1597 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1942 2010 5.01 %
Rwork0.1566 38127 -
obs0.1585 40137 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.55 Å2
Refinement stepCycle: LAST / Resolution: 1.45→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 35 155 1672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131625
X-RAY DIFFRACTIONf_angle_d1.52492202
X-RAY DIFFRACTIONf_chiral_restr0.1099238
X-RAY DIFFRACTIONf_plane_restr0.0123290
X-RAY DIFFRACTIONf_dihedral_angle_d17.5249608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.27191370.17972713X-RAY DIFFRACTION99.34
1.49-1.530.2471370.16592739X-RAY DIFFRACTION98.9
1.53-1.570.22361610.15362702X-RAY DIFFRACTION99.13
1.57-1.620.19761550.1512671X-RAY DIFFRACTION99.05
1.62-1.680.22271340.14912714X-RAY DIFFRACTION99.23
1.68-1.750.19891280.13752733X-RAY DIFFRACTION99.17
1.75-1.830.17281210.13282739X-RAY DIFFRACTION98.59
1.83-1.920.19311410.12812714X-RAY DIFFRACTION98.65
1.92-2.040.18271600.12862719X-RAY DIFFRACTION99.24
2.04-2.20.17631420.13362707X-RAY DIFFRACTION99.44
2.2-2.420.21640.14752732X-RAY DIFFRACTION99.21
2.42-2.770.20981560.17112704X-RAY DIFFRACTION99.06
2.77-3.490.19811310.17022721X-RAY DIFFRACTION97.67
3.49-47.090.17871430.1672819X-RAY DIFFRACTION99.56

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