+Open data
-Basic information
Entry | Database: PDB / ID: 5ysu | |||||||||
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Title | Plumbagin in complex with CRM1-RanM189D-RanBP1 | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Active Ran / Complex / inhibitor | |||||||||
Function / homology | Function and homology information positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / 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) ...positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / 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 / spindle pole body / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / nuclear export / 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 / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / NLS-bearing protein import into nucleus / MAPK6/MAPK4 signaling / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / ribosomal small subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / ribosomal subunit export from nucleus / nuclear pore / U1 snRNA binding / 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 / kinetochore / 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 / perinuclear region of cytoplasm / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Sun, Q. / Zhang, Y. | |||||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: RanL182A in complex with RanBP1-CRM1 Authors: Sun, Q. / Zhang, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ysu.cif.gz | 303.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ysu.ent.gz | 233.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ysu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ysu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5ysu_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5ysu_validation.xml.gz | 49.2 KB | Display | |
Data in CIF | 5ysu_validation.cif.gz | 71.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/5ysu ftp://data.pdbj.org/pub/pdb/validation_reports/ys/5ysu | HTTPS FTP |
-Related structure data
Related structure data | 5yroC 4hatS 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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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 24439.998 Da / Num. of mol.: 1 / Mutation: M189D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826 |
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#2: Protein | Mass: 16320.687 Da / Num. of mol.: 1 / Fragment: Ran Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGEX4t-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920 |
#3: Protein | Mass: 117442.812 Da / Num. of mol.: 1 / Mutation: D537G,T539C,V540E,K541Q,Y1022C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGEX4t-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822 |
-Non-polymers , 7 types, 359 molecules
#4: Chemical | ChemComp-GTP / | ||||||||
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#5: Chemical | ChemComp-MG / | ||||||||
#6: Chemical | #7: Chemical | ChemComp-NO3 / #8: Chemical | #9: Chemical | ChemComp-NA / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.68 Å3/Da / Density % sol: 54.13 % / Mosaicity: 0.287 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 18% PEG 3350, 200mM Ammonium Nitrate, 100mM Bis-Tris pH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97916 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 77361 / % possible obs: 100 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.058 / Rrim(I) all: 0.156 / Χ2: 0.981 / Net I/σ(I): 2.6 / Num. measured all: 911944 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HAT Resolution: 2.3→49.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2345 / WRfactor Rwork: 0.1985 / FOM work R set: 0.6895 / SU B: 13.19 / SU ML: 0.278 / SU R Cruickshank DPI: 0.32 / SU Rfree: 0.2297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.331 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 181.53 Å2 / Biso mean: 66.277 Å2 / Biso min: 41.14 Å2
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Refinement step | Cycle: final / Resolution: 2.3→49.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Rfactor Rfree error: 0
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