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Yorodumi- PDB-5u9j: Crystal structure of the FKBP domain of human aryl hydrocarbon re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u9j | |||||||||
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Title | Crystal structure of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) complexed with geranyl geranyl pyrophoshate | |||||||||
Components | Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) | |||||||||
Keywords | SIGNALING PROTEIN / AIPL1 / FKBP / chaperone / PDE6 / photoreceptor / LCA / isoprenyl | |||||||||
Function / homology | Function and homology information farnesylated protein binding / regulation of opsin-mediated signaling pathway / protein farnesylation / phototransduction, visible light / retina homeostasis / visual perception / photoreceptor inner segment / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / nuclear speck ...farnesylated protein binding / regulation of opsin-mediated signaling pathway / protein farnesylation / phototransduction, visible light / retina homeostasis / visual perception / photoreceptor inner segment / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / nuclear speck / apoptotic process / negative regulation of apoptotic process / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Yadav, R.P. / Gakhar, L. / Liping, Y. / Artemyev, N.O. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Unique structural features of the AIPL1-FKBP domain that support prenyl lipid binding and underlie protein malfunction in blindness. Authors: Yadav, R.P. / Gakhar, L. / Yu, L. / Artemyev, N.O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u9j.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u9j.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 5u9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/5u9j ftp://data.pdbj.org/pub/pdb/validation_reports/u9/5u9j | HTTPS FTP |
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-Related structure data
Related structure data | 5u9aSC 5u9iC 5u9kC 5v35C S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19327.109 Da / Num. of mol.: 2 / Fragment: UNP residues 2-161 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIPL1, AIPL2 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZN9 #2: Chemical | #3: Chemical | ChemComp-IPA / | #4: Chemical | ChemComp-NA / | #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: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 100 mM Na-Citrate 20%(W/V) PEG 4000 20% (V/V) 2-Propanol PH range: 5-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.152 Å / Num. obs: 17642 / % possible obs: 98.1 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.1→2.37 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 5.3 / CC1/2: 0.957 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U9A Resolution: 2.1→41.152 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.82 / Phase error: 32.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→41.152 Å
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Refine LS restraints |
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LS refinement shell |
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