+Open data
-Basic information
Entry | Database: PDB / ID: 6q82 | ||||||
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Title | Crystal structure of the biportin Pdr6 in complex with RanGTP | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Importin-Beta family / biportin / nuclear transport / GTPase | ||||||
Function / homology | Function and homology information 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 ...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 / regulation of cell size / 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 / 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 / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.994 Å | ||||||
Authors | Aksu, M. / Vera-Rodriguez, A. / Trakhanov, S. / Gorlich, D. | ||||||
Citation | Journal: J.Cell Biol. / Year: 2019 Title: Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122. Authors: Aksu, M. / Trakhanov, S. / Vera Rodriguez, A. / Gorlich, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q82.cif.gz | 498.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q82.ent.gz | 424.7 KB | Display | PDB format |
PDBx/mmJSON format | 6q82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/6q82 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/6q82 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 124711.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: KAP122, PDR6, YGL016W / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 F' / References: UniProt: P32767 |
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#2: Protein | Mass: 20192.484 Da / Num. of mol.: 1 / Mutation: Q69L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 F' / References: UniProt: P62826 |
#3: Chemical | ChemComp-GTP / |
#4: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.44 Å3/Da / Density % sol: 72.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.26 Details: Pentaerythritol propoxylate (17/8 PO/OH), MPD, Sodium acetate, Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97796 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97796 Å / Relative weight: 1 |
Reflection | Resolution: 2.994→59.894 Å / Num. obs: 51160 / % possible obs: 99.7 % / Redundancy: 399.8 % / Biso Wilson estimate: 106.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.2728 / Rpim(I) all: 0.01361 / Net I/σ(I): 44.7 |
Reflection shell | Resolution: 2.994→3.101 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4876 / CC1/2: 0.893 / % possible all: 97.42 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.994→59.894 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 332.1 Å2 / Biso mean: 111.0655 Å2 / Biso min: 46.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.994→59.894 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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