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Open data
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Basic information
Entry | Database: PDB / ID: 7dbg | ||||||
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Title | Yeast CRM1e (apo) in complex with Ran-RanBP1 | ||||||
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![]() | TRANSPORT PROTEIN / Complex | ||||||
Function / homology | ![]() positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / import into nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding ...positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / import into nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / 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 / 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 / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sun, Q. / Lei, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Novel Mechanistic Observations and NES-Binding Groove Features Revealed by the CRM1 Inhibitors Plumbagin and Oridonin. Authors: Lei, Y. / Li, Y. / Tan, Y. / Qian, Z. / Zhou, Q. / Jia, D. / 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 | ![]() | 300.1 KB | Display | ![]() |
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PDB format | ![]() | 232.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 909.2 KB | Display | ![]() |
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Full document | ![]() | 924.8 KB | Display | |
Data in XML | ![]() | 51.6 KB | Display | |
Data in CIF | ![]() | 75.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m60C ![]() 6m6xSC 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 on special symmetry positions |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 24400.039 Da / Num. of mol.: 1 / Mutation: Q69L, L182A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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.) ![]() ![]() Gene: YRB1, GI526_G0000915 / Production host: ![]() ![]() |
#3: Protein | Mass: 115224.461 Da / Num. of mol.: 1 Mutation: S27E , Q49E, A51V, del377-413, del441-461, D537G, T539C, V540E, K541Q, S553R, Q561E, A741T, Y1022C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CRM1, GI526_G0002640, PACBIOSEQ_LOCUS2878, PACBIOSEQ_LOCUS3002 Production host: ![]() ![]() |
-Non-polymers , 7 types, 619 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / | ||||||||||
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#5: Chemical | #6: Chemical | ChemComp-GTP / | #7: Chemical | ChemComp-CL / #8: Chemical | #9: Chemical | ChemComp-MPO / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.03 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and ...Details: 0.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and MOPS), and 50 % Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→30.12 Å / Num. obs: 107784 / % possible obs: 100 % / Redundancy: 25.2 % / CC1/2: 0.999 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.06→2.11 Å / Num. unique obs: 7866 / CC1/2: 0.71 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6m6x Resolution: 2.06→30.12 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.204 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.16 / 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: 130.83 Å2 / Biso mean: 47.923 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 2.06→30.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.113 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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