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Open data
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Basic information
Entry | Database: PDB / ID: 8huf | ||||||
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Title | B28 in complex with CRM1-Ran-RanBP1 | ||||||
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Function / homology | ![]() 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 ...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 / nucleocytoplasmic transport / dynein intermediate chain binding / DNA metabolic process / mitotic sister chromatid segregation / spermatid development / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sun, Q. / Lei, Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: B28 in complex with CRM1-Ran-RanBP1 Authors: Sun, Q. / Lei, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 561.3 KB | Display | ![]() |
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PDB format | ![]() | 454.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cndS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 24399.055 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 , 8 types, 459 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/N5X.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/N5X.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / | ||||||||||||
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#5: Chemical | ![]() #6: Chemical | ChemComp-GTP / | ![]() #7: Chemical | ChemComp-BR / | ![]() #8: Chemical | ChemComp-CL / | ![]() #9: Chemical | ChemComp-NA / | #10: Chemical | ChemComp-N5X / | #11: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.47 % |
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Crystal grow![]() | Temperature: 293 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: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||
Reflection | Resolution: 2.29→152.35 Å / Num. obs: 79793 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.037 / Rrim(I) all: 0.19 / Net I/σ(I): 13.1 / Num. measured all: 2097123 / Scaling rejects: 24072 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7CND Resolution: 2.29→100.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.473 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.2 / 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: 47.858 Å2
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Refinement step | Cycle: 1 / Resolution: 2.29→100.62 Å
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