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Yorodumi- PDB-4ol0: Crystal structure of transportin-SR2, a karyopherin involved in h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ol0 | ||||||
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Title | Crystal structure of transportin-SR2, a karyopherin involved in human disease, in complex with Ran | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Human Karyopherins / Active Transport / Nucleus / ran GTP-Binding Protein | ||||||
Function / homology | Function and homology information annulate lamellae / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA ...annulate lamellae / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / dynein intermediate chain binding / DNA metabolic process / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / nuclear pore / centriole / protein export from nucleus / viral process / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Tsirkone, V.G. / Strelkov, S.V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Structure of transportin SR2, a karyopherin involved in human disease, in complex with Ran. Authors: Tsirkone, V.G. / Beutels, K.G. / Demeulemeester, J. / Debyser, Z. / Christ, F. / Strelkov, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ol0.cif.gz | 445.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ol0.ent.gz | 364.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ol0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/4ol0 ftp://data.pdbj.org/pub/pdb/validation_reports/ol/4ol0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24456.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pETSUK / Production host: Escherichia coli (E. coli) / References: UniProt: P62826 |
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#2: Protein | Mass: 104052.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO3, IPO12 / Plasmid: pETSUK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5L0 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GTP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 100mM MES, 4.8% MPD, 15.2% PEG6000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→44.18 Å / Num. obs: 27515 / % possible obs: 99.3 % |
Reflection shell | Highest resolution: 2.9 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→44.184 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 28.14 / 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: 2.9→44.184 Å
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Refine LS restraints |
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LS refinement shell |
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