+Open data
-Basic information
Entry | Database: PDB / ID: 4wvf | ||||||
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Title | Crystal structure of KPT276 in complex with CRM1-Ran-RanBP1 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/TRANSPORT PROTEIN INHIBITOR / CRM1 / inhibitor / SINE / KPT / TRANSPORT PROTEIN-TRANSPORT PROTEIN INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus / Regulation of HSF1-mediated heat shock response / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / SUMOylation of SUMOylation proteins ...positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus / Regulation of HSF1-mediated heat shock response / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / SUMOylation of RNA binding proteins / 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 / RNA export from nucleus / SUMOylation of chromatin organization proteins / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / dynein intermediate chain binding / NLS-bearing protein import into nucleus / 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 / GTPase activator activity / 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 / G1/S transition of mitotic cell cycle / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Sun, Q. / Chook, Y. | ||||||
Citation | Journal: Nat.Neurosci. / Year: 2015 Title: Nuclear export inhibitors avert progression in preclinical models of inflammatory demyelination. Authors: Haines, J.D. / Herbin, O. / de la Hera, B. / Vidaurre, O.G. / Moy, G.A. / Sun, Q. / Fung, H.Y. / Albrecht, S. / Alexandropoulos, K. / McCauley, D. / Chook, Y.M. / Kuhlmann, T. / Kidd, G.J. / ...Authors: Haines, J.D. / Herbin, O. / de la Hera, B. / Vidaurre, O.G. / Moy, G.A. / Sun, Q. / Fung, H.Y. / Albrecht, S. / Alexandropoulos, K. / McCauley, D. / Chook, Y.M. / Kuhlmann, T. / Kidd, G.J. / Shacham, S. / Casaccia, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wvf.cif.gz | 638.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wvf.ent.gz | 513.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wvf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4wvf_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4wvf_validation.xml.gz | 61.2 KB | Display | |
Data in CIF | 4wvf_validation.cif.gz | 95.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/4wvf ftp://data.pdbj.org/pub/pdb/validation_reports/wv/4wvf | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
-Protein , 3 types, 3 molecules ABC
#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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62826 |
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#2: Protein | Mass: 16320.687 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Production host: Escherichia coli (E. coli) / References: UniProt: P41920 |
#3: Protein | Mass: 117471.922 Da / Num. of mol.: 1 / Mutation: T539C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: R008 / Gene: Crm1, R008_G21866 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W7PTE1 |
-Non-polymers , 7 types, 1381 molecules
#4: Chemical | ChemComp-GNP / | ||||||||
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#5: Chemical | ChemComp-MG / | ||||||||
#6: Chemical | #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-K76 / ( | #9: Chemical | #10: 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: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 0.1M Bis-Tris pH 6.6, 0.2M NH4NO3 and 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 159687 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.068 / Χ2: 1.362 / Net I/av σ(I): 33.892 / Net I/σ(I): 9.7 / Num. measured all: 1188877 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 6.846 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 354.49 Å2 / Biso mean: 45.781 Å2 / Biso min: 22.98 Å2
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Refinement step | Cycle: final / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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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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