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- PDB-9nem: Structure of Unc119-Farnesylated peptide complex -

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Basic information

Entry
Database: PDB / ID: 9nem
TitleStructure of Unc119-Farnesylated peptide complex
ComponentsProtein unc-119 homolog A
KeywordsTRANSPORT PROTEIN / Unc119
Function / homology
Function and homology information


negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / lipoprotein transport / positive regulation of protein tyrosine kinase activity / spindle midzone / mitotic cytokinesis / phototransduction / intercellular bridge / visual perception / endocytosis ...negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / lipoprotein transport / positive regulation of protein tyrosine kinase activity / spindle midzone / mitotic cytokinesis / phototransduction / intercellular bridge / visual perception / endocytosis / spindle pole / nervous system development / chemical synaptic transmission / synapse / lipid binding / centrosome / cytosol
Similarity search - Function
: / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Immunoglobulin E-set
Similarity search - Domain/homology
FARNESYL / Protein unc-119 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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
DepositionFeb 20, 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

Downloads & links

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Assembly

Deposited unit
A: Protein unc-119 homolog A
B: Protein unc-119 homolog A
C: Protein unc-119 homolog A
D: Protein unc-119 homolog A
E: Protein unc-119 homolog A
F: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,18211
Polymers138,1506
Non-polymers1,0325
Water1,76598
1
A: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2312
Polymers23,0251
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2312
Polymers23,0251
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2312
Polymers23,0251
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2312
Polymers23,0251
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2312
Polymers23,0251
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Protein unc-119 homolog A


Theoretical massNumber of molelcules
Total (without water)23,0251
Polymers23,0251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.159, 81.039, 192.330
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

#1: Protein
Protein unc-119 homolog A / Retinal protein 4 / hRG4


Mass: 23025.021 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNC119, RG4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13432
#2: Chemical
ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C15H26 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 44.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate, pH 4.5-5.5, 200 mM ammonium acetate, 20-30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.49→49.82 Å / Num. obs: 43838 / % possible obs: 99.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.87 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.7
Reflection shellResolution: 2.49→2.58 Å / Num. unique obs: 4570 / CC1/2: 0.734

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→49.82 Å / SU ML: 0.4035 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.9541
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2949 2160 4.99 %
Rwork0.263 41134 -
obs0.2646 43294 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.47 Å2
Refinement stepCycle: LAST / Resolution: 2.49→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8309 0 75 98 8482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00288619
X-RAY DIFFRACTIONf_angle_d0.551111617
X-RAY DIFFRACTIONf_chiral_restr0.04551191
X-RAY DIFFRACTIONf_plane_restr0.00411526
X-RAY DIFFRACTIONf_dihedral_angle_d14.09473237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.44461420.38882764X-RAY DIFFRACTION99.93
2.55-2.610.4161400.36532760X-RAY DIFFRACTION99.97
2.61-2.680.50171410.43842611X-RAY DIFFRACTION95.62
2.68-2.760.41491220.34892751X-RAY DIFFRACTION98.73
2.76-2.850.28061300.28782790X-RAY DIFFRACTION99.97
2.85-2.950.31451480.28422749X-RAY DIFFRACTION99.86
2.95-3.070.34761310.28522791X-RAY DIFFRACTION99.83
3.07-3.210.31761420.30222761X-RAY DIFFRACTION99.9
3.21-3.380.38071640.29632769X-RAY DIFFRACTION99.97
3.38-3.590.29361370.30772679X-RAY DIFFRACTION95.85
3.59-3.870.33231460.34092418X-RAY DIFFRACTION87.12
3.87-4.260.31131400.23982635X-RAY DIFFRACTION93.88
4.26-4.870.19761530.1712817X-RAY DIFFRACTION99.87
4.87-6.140.21251510.18012862X-RAY DIFFRACTION99.9
6.14-49.820.23031730.20822977X-RAY DIFFRACTION99.75
Refinement TLS params.Method: refined / Origin x: 17.5575566151 Å / Origin y: 1.75560305193 Å / Origin z: -20.8427874611 Å
111213212223313233
T0.246184874151 Å20.0154348447026 Å2-0.00871144251414 Å2-0.220861043221 Å20.00498601729201 Å2--0.234238241643 Å2
L0.200530938525 °20.0552044948474 °2-0.0811512421165 °2--0.0231338679667 °2-0.0775688064429 °2--0.0838400341437 °2
S0.00534138772824 Å °0.0651891710561 Å °-0.00540903698257 Å °0.0288549069602 Å °-0.00285921390055 Å °0.0206308304108 Å °-0.00370314050269 Å °-0.0128043006655 Å °-2.5791925331E-7 Å °
Refinement TLS groupSelection details: all

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