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Open data
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Basic information
Entry | Database: PDB / ID: 5ytb | ||||||
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Title | RanY197A in complex with RanBP1-CRM1 | ||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sun, Q. / Zhang, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: RanY197A in complex with RanBP1-CRM1 Authors: Sun, Q. / Zhang, 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 | ![]() | 571.6 KB | Display | ![]() |
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PDB format | ![]() | 460.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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: 24364.010 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: 16249.607 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: 116682.086 Da / Num. of mol.: 1 / Mutation: D537G, T539C, V540E, K541Q, Y1022C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: ![]() ![]() ![]() |
-Non-polymers , 7 types, 244 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GTP / ![]() | ||||||
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#5: Chemical | ChemComp-MG / | ||||||
#6: Chemical | ChemComp-EDO / ![]() | ||||||
#7: Chemical | ChemComp-CL / ![]() #8: Chemical | ![]() #9: Chemical | ![]() #10: Water | ChemComp-HOH / | ![]() |
-Details
Sequence details | Natural mutation at this position |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.33 % |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 77397 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.028 / Rrim(I) all: 0.099 / Χ2: 0.974 / Net I/σ(I): 5.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 16.554 / SU ML: 0.173 / SU R Cruickshank DPI: 0.1851 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.211 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.9 Å2 / Biso mean: 66.292 Å2 / Biso min: 34.89 Å2
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Refinement step | Cycle: final / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.361 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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