+Open data
-Basic information
Entry | Database: PDB / ID: 7umo | ||||||
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Title | Structure of Unc119-inhibitor complex. | ||||||
Components | Protein unc-119 homolog A | ||||||
Keywords | TRANSPORT PROTEIN / Unc119 / inhibitor | ||||||
Function / homology | Function and homology information negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / lipoprotein transport / intercellular bridge / phototransduction / mitotic cytokinesis / positive regulation of protein tyrosine kinase activity / spindle midzone / visual perception / spindle pole ...negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / lipoprotein transport / intercellular bridge / phototransduction / mitotic cytokinesis / positive regulation of protein tyrosine kinase activity / spindle midzone / visual perception / spindle pole / endocytosis / nervous system development / chemical synaptic transmission / centrosome / lipid binding / synapse / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Srivastava, D. / Sebag, J.A. / Artemyev, N.O. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7umo.cif.gz | 516.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7umo.ent.gz | 355.7 KB | Display | PDB format |
PDBx/mmJSON format | 7umo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/7umo ftp://data.pdbj.org/pub/pdb/validation_reports/um/7umo | HTTPS FTP |
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-Related structure data
Related structure data | 3rbqS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | 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 / ( #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Cacodylate, Sodium acetate, PEG4000 / PH range: 6.5-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0722 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→48.16 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1
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