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- PDB-7umo: Structure of Unc119-inhibitor complex. -

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Basic information

Entry
Database: PDB / ID: 7umo
TitleStructure of Unc119-inhibitor complex.
ComponentsProtein unc-119 homolog A
KeywordsTRANSPORT PROTEIN / Unc119 / inhibitor
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
Chem-NT6 / Protein unc-119 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSrivastava, D. / Sebag, J.A. / Artemyev, N.O.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Cell Chem Biol / Year: 2023
Title: Insulin sensitization by small molecules enhancing GLUT4 translocation.
Authors: Yin, T.C. / Van Vranken, J.G. / Srivastava, D. / Mittal, A. / Buscaglia, P. / Moore, A.E. / Verdinez, J.A. / Graham, A.E. / Walsh, S.A. / Acevedo, M.A. / Kerns, R.J. / Artemyev, N.O. / Gygi, S.P. / Sebag, J.A.
History
DepositionApr 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)140,37815
Polymers138,1506
Non-polymers2,2289
Water4,053225
1
A: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5344
Polymers23,0251
Non-polymers5093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3502
Polymers23,0251
Non-polymers3251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3502
Polymers23,0251
Non-polymers3251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3502
Polymers23,0251
Non-polymers3251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4423
Polymers23,0251
Non-polymers4172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3502
Polymers23,0251
Non-polymers3251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.820, 78.130, 187.070
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-NT6 / (3s,5s,7s)-N-(4,5-dichloropyridin-2-yl)adamantane-1-carboxamide


Mass: 325.233 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H18Cl2N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Cacodylate, Sodium acetate, PEG4000 / PH range: 6.5-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0722 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.3→48.16 Å / Num. obs: 50240 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 40.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.025 / Rrim(I) all: 0.093 / Χ2: 1.05 / Net I/σ(I): 20.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 14 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4543 / CC1/2: 0.947 / Rpim(I) all: 0.191 / Rrim(I) all: 0.719 / Χ2: 0.86 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RBQ

3rbq


Resolution: 2.3→48.16 Å / SU ML: 0.2831 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2424 2544 5.07 %
Rwork0.1966 47607 -
obs0.1989 50151 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.41 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8266 0 144 225 8635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00388681
X-RAY DIFFRACTIONf_angle_d0.808411742
X-RAY DIFFRACTIONf_chiral_restr0.05191209
X-RAY DIFFRACTIONf_plane_restr0.00662566
X-RAY DIFFRACTIONf_dihedral_angle_d12.49573327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.2631120.23172596X-RAY DIFFRACTION99.93
2.34-2.390.32571170.22772620X-RAY DIFFRACTION100
2.39-2.440.30221180.22762662X-RAY DIFFRACTION99.93
2.44-2.50.35651400.24182584X-RAY DIFFRACTION99.96
2.5-2.560.30831430.23862623X-RAY DIFFRACTION100
2.56-2.630.28021330.22632629X-RAY DIFFRACTION99.78
2.63-2.710.25491470.21612622X-RAY DIFFRACTION99.96
2.71-2.80.27841450.22452611X-RAY DIFFRACTION99.93
2.8-2.90.30791520.24362603X-RAY DIFFRACTION99.96
2.9-3.010.29561500.23282619X-RAY DIFFRACTION99.96
3.01-3.150.28571380.23062626X-RAY DIFFRACTION99.93
3.15-3.320.25681470.21782628X-RAY DIFFRACTION100
3.32-3.520.28741260.1912666X-RAY DIFFRACTION100
3.52-3.80.21191480.18032659X-RAY DIFFRACTION99.89
3.8-4.180.19721830.16212622X-RAY DIFFRACTION99.86
4.18-4.780.17331520.1482674X-RAY DIFFRACTION100
4.78-6.020.2191350.16942735X-RAY DIFFRACTION99.93
6.02-48.160.24031580.21222828X-RAY DIFFRACTION99.33
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)
11.149477159050.5891726150260.02007793660161.379333103890.2755248572011.22502362469-0.0135946519448-0.0873811956931-0.0124746280984-0.1019741340370.0712328475495-0.0224793710614-0.09893909803010.1239103676931.41257046402E-50.2720763712920.01041259932560.03736836366860.275360175533-0.01041494311970.2717315965934.28432563308-20.90526657921.3373213189
20.4803504855-0.457150021245-0.277508924991.24969004722-0.6984986485471.847310557220.08337389816950.0416271313627-0.07000446940390.314418715229-0.007721954463210.116568182313-0.276530128857-0.02192360798960.03712920996550.2964413241950.03703857073520.05517895196810.2845638620260.02123110946410.2737655616589.41084881324-15.3067552579-10.0672131597
31.607223091550.6255127159120.5693819902280.938609488196-0.7583755410842.701815542040.184344302134-0.258179221016-0.156900752499-0.312316507108-0.05302192285470.008308467741481.041045850120.2325551674680.551066863410.5364490556410.117346792391-0.03620179824190.2829809098620.04093109632740.2913897231638.07248571626-53.1633521859.58056941398
41.46486737974-0.3539334691120.1792507534720.679277376702-0.1172959305711.352848422110.0159112971555-0.166527953367-0.1338105868-0.07798401742860.0314808922582-0.02059982016410.275171573121-0.3768365779150.01629535771890.283274496969-0.106166032098-0.03619833137430.3764179634090.04164872974220.29197220599444.0130581696-34.601557076240.7275371913
52.19984349322-0.704462925181-0.3285032689871.1301365430.364286230832.09806711057-0.01413822030240.1052419216750.339607600092-0.2527948239960.0920511737361-0.0368479090070.0655284289225-0.1529469510530.03671005189550.1445789255830.0238822619716-0.02859848804640.2532290554790.05502099350520.3140481183562.69462090449-58.144024834640.8576242031
60.7484642898730.5654881424370.2226713617431.63973740710.9170276685442.46879179123-0.102591934735-0.0742110059017-0.0632809635185-0.337892915120.0585739429880.0931813381312-0.470353169436-0.101642442314-0.01428114759890.5047164344350.0107914803046-0.01078897968690.3276125622010.009647501850190.33330480629338.2081665917-70.487588662621.3817944425
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain AAA - D59 - 402
22chain BBE - F60 - 301
33chain CCG - H60 - 301
44chain DDI - J58 - 301
55chain EEK - M59 - 401
66chain FFN - O59 - 301

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