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Yorodumi- PDB-4hay: Crystal structure of CRM1 inhibitor Leptomycin B in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 4hay | ||||||
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Title | Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1(K548E,K579Q)-Ran-RanBP1 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/ANTIBIOTIC / HEAT repeat / nuclear export / Ran-RanBP1 / LMB / leptomycin B / PROTEIN TRANSPORT-ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information positive regulation of mitotic centrosome separation / MAPK6/MAPK4 signaling / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA nuclear export complex / Regulation of HSF1-mediated heat shock response / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette ...positive regulation of mitotic centrosome separation / MAPK6/MAPK4 signaling / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA nuclear export complex / Regulation of HSF1-mediated heat shock response / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / SUMOylation of SUMOylation proteins / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / SUMOylation of RNA binding proteins / spindle pole body / protein localization to kinetochore / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / nuclear export / Nuclear import of Rev protein / GTP metabolic process / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMOylation of chromatin organization proteins / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / dynein intermediate chain binding / DNA metabolic process / NLS-bearing protein import into nucleus / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA 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 / G1/S transition of mitotic cell cycle / recycling endosome / kinetochore / 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 / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Sun, Q. / Chook, Y.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Nuclear export inhibition through covalent conjugation and hydrolysis of Leptomycin B by CRM1. Authors: Sun, Q. / Carrasco, Y.P. / Hu, Y. / Guo, X. / Mirzaei, H. / Macmillan, J. / Chook, Y.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hay.cif.gz | 578.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hay.ent.gz | 484 KB | Display | PDB format |
PDBx/mmJSON format | 4hay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/4hay ftp://data.pdbj.org/pub/pdb/validation_reports/ha/4hay | HTTPS FTP |
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-Related structure data
Related structure data | 4hatC 4hauC 4havC 4hawC 4haxC 4hazC 4hb0C 4hb2C 4hb3C 4hb4C 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: 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) / References: UniProt: P62826 |
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#2: Protein | Mass: 16378.788 Da / Num. of mol.: 1 / Fragment: RanDB1 (UNP residues 62-201) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Production host: Escherichia coli (E. coli) / References: UniProt: P41920 |
#3: Protein | Mass: 117397.750 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: T539C,K548E,K579Q,Y1022C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: Escherichia coli (E. coli) / References: UniProt: P30822 |
-Non-polymers , 6 types, 639 molecules
#4: Chemical | ChemComp-GNP / | ||||||
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#5: Chemical | ChemComp-MG / | ||||||
#6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-LMB / | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Sequence details | CHAIN C COMPRISES RESIDUES 1-376 AND 414-1058 OF EXPORTIN-1 (UNP P30822) WITH RESIDUES 377-413 DELETED. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 18% PEG3350, 200 mM ammonium nitrate, 100 mM Bis-Tris, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 77568 / Num. obs: 75939 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 13.977 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 46.689 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 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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