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Open data
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Basic information
Entry | Database: PDB / ID: 1ksj | ||||||
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Title | Complex of Arl2 and PDE delta, Crystal Form 2 (SeMet) | ||||||
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![]() | SIGNALING PROTEIN/HYDROLASE / small GTPase / small GTP-binding protein / Arf family / effector molecule / immunoglobuline-like fold / GDI / SIGNALING PROTEIN-HYDROLASE COMPLEX | ||||||
Function / homology | ![]() Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / acetylcholine transport / ARL13B-mediated ciliary trafficking of INPP5E / RAS processing / GTPase inhibitor activity / bicellular tight junction assembly / maintenance of protein location in nucleus / response to stimulus / centrosome cycle / positive regulation of cell-substrate adhesion ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / acetylcholine transport / ARL13B-mediated ciliary trafficking of INPP5E / RAS processing / GTPase inhibitor activity / bicellular tight junction assembly / maintenance of protein location in nucleus / response to stimulus / centrosome cycle / positive regulation of cell-substrate adhesion / regulation of glycolytic process / negative regulation of GTPase activity / regulation of aerobic respiration / regulation of microtubule polymerization / lateral plasma membrane / positive regulation of microtubule polymerization / visual perception / cytoplasmic vesicle membrane / mitochondrial intermembrane space / small GTPase binding / cilium / RAS processing / GDP binding / microtubule cytoskeleton / protein folding / cytoplasmic vesicle / cytoskeleton / focal adhesion / GTPase activity / centrosome / nucleolus / GTP binding / Golgi apparatus / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hanzal-Bayer, M. / Renault, L. / Roversi, P. / Wittinghofer, A. / Hillig, R.C. | ||||||
![]() | ![]() Title: The complex of Arl2-GTP and PDE delta: from structure to function Authors: Hanzal-Bayer, M. / Renault, L. / Roversi, P. / Wittinghofer, A. / Hillig, R.C. #1: ![]() Title: Coexpression, copurification, crystallization and preliminary X-ray analysis of a complex of Arl2-GTP and PDE delta Authors: Renault, L. / Hanzal-Bayer, M. / Hillig, R.C. #2: ![]() Title: Structural and biochemical properties show Arl3-GDP as a distinct GTP-binding protein Authors: Hillig, R.C. / Hanzal-Bayer, M. / Linari, M. / Becker, J. / Wittinghofer, A. / Renault, L. #3: ![]() Title: The delta subunit of rod specific cyclic GMP phosphodiesterase, PDE delta, interacts with the Arf-like protein Arl3 in a GTP specific manner Authors: Linari, M. / Hanzal-Bayer, M. / Becker, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.9 KB | Display | ![]() |
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PDB format | ![]() | 62.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 995.8 KB | Display | ![]() |
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Full document | ![]() | 1016.5 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The deposited coordinates represent the biological assembly (consisting of one Arl2 molecule (bound to GDP/PO4) and one PDE delta molecule). |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 21297.752 Da / Num. of mol.: 1 / Mutation: S33L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 17895.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O43924, 3',5'-cyclic-nucleotide phosphodiesterase |
-Non-polymers , 6 types, 110 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PO4 / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-BME / |
#6: Chemical | ChemComp-GDP / |
#7: Chemical | ChemComp-GTP / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 5000 MME, HEPES, MgCl2, beta mercaptoethanol, GTP, PEG 400 as cryo protectant, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 9, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.8 Å / Num. all: 9926 / Num. obs: 9926 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 56 Å2 / Rsym value: 0.081 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 2.6→2.65 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 7 / Num. unique all: 558 / Rsym value: 0.391 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: combination of Molecular Replacement, SAD phasing Starting model: human Arf1-GppNHp, N-terminally truncated by 17 residues (J. Goldberg, Cell. 95:237-248, 1998) Resolution: 2.6→19.8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 43.6 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å
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