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Yorodumi- PDB-4goj: The Crystal Structure of full length Arl3GppNHp in complex with U... -
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-Basic information
Entry | Database: PDB / ID: 4goj | ||||||
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Title | The Crystal Structure of full length Arl3GppNHp in complex with UNC119a | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Small G protein Arl / GDI-like solubilizing factors / Cilia | ||||||
Function / homology | Function and homology information negative regulation of caveolin-mediated endocytosis / Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / negative regulation of clathrin-dependent endocytosis / protein localization to ciliary membrane / intraciliary transport / ciliary transition zone / post-Golgi vesicle-mediated transport / photoreceptor connecting cilium / Golgi to plasma membrane transport ...negative regulation of caveolin-mediated endocytosis / Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / negative regulation of clathrin-dependent endocytosis / protein localization to ciliary membrane / intraciliary transport / ciliary transition zone / post-Golgi vesicle-mediated transport / photoreceptor connecting cilium / Golgi to plasma membrane transport / protein localization to cilium / lipoprotein transport / smoothened signaling pathway / small GTPase-mediated signal transduction / intercellular bridge / cytoplasmic microtubule / axoneme / mitotic cytokinesis / phototransduction / cilium assembly / spindle midzone / positive regulation of protein tyrosine kinase activity / visual perception / ciliary basal body / kidney development / spindle microtubule / cilium / spindle pole / endocytosis / GDP binding / microtubule cytoskeleton / protein transport / nervous system development / midbody / chemical synaptic transmission / microtubule binding / Golgi membrane / GTPase activity / centrosome / synapse / lipid binding / GTP binding / Golgi apparatus / magnesium ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ismail, S. / Xiang-Chen, Y. / Miertzschke, M. / Vetter, I. / Koerner, C. / Wittinghofer, A. | ||||||
Citation | Journal: Embo J. / Year: 2012 Title: Structural basis for Arl3-specific release of myristoylated ciliary cargo from UNC119. Authors: Ismail, S.A. / Chen, Y.X. / Miertzschke, M. / Vetter, I.R. / Koerner, C. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4goj.cif.gz | 154.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4goj.ent.gz | 120 KB | Display | PDB format |
PDBx/mmJSON format | 4goj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/4goj ftp://data.pdbj.org/pub/pdb/validation_reports/go/4goj | HTTPS FTP |
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-Related structure data
Related structure data | 4gokC 3bh6S 3gqqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21469.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arl3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WUL7 #2: Protein | Mass: 26996.385 Da / Num. of mol.: 2 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 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.4 M Sodium Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 29, 2012 |
Radiation | Monochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.97 Å / Num. all: 51107 / Num. obs: 51107 / % possible obs: 99.6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.06 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 5.53 % / Rmerge(I) obs: 0.395 / Num. unique all: 6574 / Rsym value: 0.383 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BH6, 3GQQ Resolution: 2.1→29.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.065 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.952 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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