+Open data
-Basic information
Entry | Database: PDB / ID: 5yu6 | |||||||||||||||
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Title | CRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX | |||||||||||||||
Components |
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Keywords | RNA BINDING PROTEIN/NUCLEAR PROTEIN / RNA BINDING PROTEIN-NUCLEAR PROTEIN COMPLEX | |||||||||||||||
Function / homology | Function and homology information RISC complex binding / pre-miRNA binding / RNA nuclear export complex / nuclear export signal receptor activity / miRNA metabolic process / pre-miRNA export from nucleus / snRNA import into nucleus / RNA export from nucleus / RISC complex / GTP metabolic process ...RISC complex binding / pre-miRNA binding / RNA nuclear export complex / nuclear export signal receptor activity / miRNA metabolic process / pre-miRNA export from nucleus / snRNA import into nucleus / RNA export from nucleus / RISC complex / GTP metabolic process / MicroRNA (miRNA) biogenesis / ribosomal subunit export from nucleus / mitotic sister chromatid segregation / protein export from nucleus / positive regulation of protein export from nucleus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / small GTPase binding / protein import into nucleus / melanosome / nuclear envelope / tRNA binding / cell division / mRNA binding / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) unidentified (others) Canis lupus familiaris (dog) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.997 Å | |||||||||||||||
Authors | Yamazawa, R. / Jiko, C. / Lee, S.J. / Yamashita, E. | |||||||||||||||
Funding support | Japan, Korea, Republic Of, 4items
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Citation | Journal: Structure / Year: 2018 Title: Structural Basis for Selective Binding of Export Cargoes by Exportin-5 Authors: Yamazawa, R. / Jiko, C. / Choi, S. / Park, I.Y. / Nakagawa, A. / Yamashita, E. / Lee, S.J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yu6.cif.gz | 1003.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yu6.ent.gz | 825.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/5yu6 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yu6 | HTTPS FTP |
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-Related structure data
Related structure data | 5yu7C 3a6pS 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
#1: Protein | Mass: 136454.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XPO5, KIAA1291, RANBP21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HAV4 #2: Protein/peptide | Mass: 1124.378 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) #3: Protein | Mass: 24456.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: RAN / Production host: Escherichia coli (E. coli) / References: UniProt: P62825 #4: Chemical | #5: Chemical | Sequence details | REGARDING THE RESIDUES AT POSITION 1305-1317 (CHAINS E/F), THE AUTHORS DO NOT KNOW EACH SEQUENCE. ...REGARDING THE RESIDUES AT POSITION 1305-1317 (CHAINS E/F), THE AUTHORS DO NOT KNOW EACH SEQUENCE. IN ADDITION, THEY COULDN'T SPECIFY ALL OF THE AMINO ACIDS DUE TO THE DISCONTINU | |
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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: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, DTT, MgCl2, spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Feb 8, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3→83.33 Å / Num. obs: 55602 / % possible obs: 82.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5227 / % possible all: 77.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A6P Resolution: 2.997→48.977 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 28.89 / 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: 2.997→48.977 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 33.9016 Å / Origin y: 60.0422 Å / Origin z: 26.4587 Å
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Refinement TLS group | Selection details: all |