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Open data
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Basic information
Entry | Database: PDB / ID: 6a3e | ||||||
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Title | MVM NES mutant Nm15 in complex with CRM1-Ran-RanBP1 | ||||||
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![]() | TRANSPORT PROTEIN / nuclear export / complex / mutant / inhibitor | ||||||
Function / homology | ![]() exit of virus from host cell nucleus through nuclear pore / Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / 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 ...exit of virus from host cell nucleus through nuclear pore / Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / 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 / tRNA export from nucleus / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / 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 / spindle pole body / 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 subunit export from nucleus / U2 snRNA binding / mRNA export from nucleus / U6 snRNA binding / nuclear pore / ribosomal small subunit export from nucleus / U1 snRNA binding / centriole / viral process / protein export from nucleus / 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 / host cell nucleus / 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 | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sun, Q. / Li, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cancer Therapy with Nanoparticle-Medicated Intracellular Expression of Peptide CRM1-Inhibitor. Authors: Sui, M. / Xiong, M. / Li, Y. / Zhou, Q. / Shen, X. / Jia, D. / Gou, M. / Sun, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 570.5 KB | Display | ![]() |
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PDB format | ![]() | 463.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6a38C ![]() 6a3aC ![]() 6a3bC ![]() 6a3cC ![]() 6kftC ![]() 4hatS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 26404.184 Da / Num. of mol.: 1 / Mutation: Y197A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 16521.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Production host: ![]() ![]() |
#3: Protein | Mass: 115052.273 Da / Num. of mol.: 1 Mutation: D537G, T539C, V540E, K541Q, Y1022C, 377-413 deletion, 441-461 deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 2482.589 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 305 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GTP / |
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#6: Chemical | ChemComp-MG / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% PEG3350, 200mM Ammonium Nitrate, 100mM Bis-Tris pH6.6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 49549 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.077 / Rrim(I) all: 0.209 / Χ2: 0.936 / Net I/σ(I): 2.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HAT Resolution: 2.7→47.31 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU B: 31.176 / SU ML: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.086 / ESU R Free: 0.328 / 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: 190.61 Å2 / Biso mean: 72.922 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.7→47.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / 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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