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Open data
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Basic information
Entry | Database: PDB / ID: 3wyg | ||||||
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Title | Crystal structure of Xpo1p-PKI-Gsp1p-GTP complex | ||||||
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![]() | GTP-BINDING PROTEIN/GTP-BINDING PROTEIN INHIBITOR / HEAT REPEAT / NUCLEAR EXPORT / GTP-BINDING PROTEIN-GTP-BINDING PROTEIN INHIBITOR COMPLEX | ||||||
Function / homology | ![]() regulation of cell cycle phase transition / Transcriptional and post-translational regulation of MITF-M expression and activity / Postmitotic nuclear pore complex (NPC) reformation / regulation of nucleocytoplasmic transport / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA re-export from nucleus / negative regulation of cAMP/PKA signal transduction / nuclear export signal receptor activity / negative regulation of cAMP-dependent protein kinase activity / tRNA export from nucleus ...regulation of cell cycle phase transition / Transcriptional and post-translational regulation of MITF-M expression and activity / Postmitotic nuclear pore complex (NPC) reformation / regulation of nucleocytoplasmic transport / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA re-export from nucleus / negative regulation of cAMP/PKA signal transduction / nuclear export signal receptor activity / negative regulation of cAMP-dependent protein kinase activity / tRNA export from nucleus / protein localization to kinetochore / U4 snRNA binding / nuclear export / cAMP-dependent protein kinase inhibitor activity / spindle pole body / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / negative regulation of protein import into nucleus / nucleus organization / MAPK6/MAPK4 signaling / protein kinase A catalytic subunit binding / ribosomal large subunit export from nucleus / U5 snRNA binding / ribosomal subunit export from nucleus / U2 snRNA binding / mRNA export from nucleus / U6 snRNA binding / ribosomal small subunit export from nucleus / U1 snRNA binding / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / kinetochore / small GTPase binding / protein import into nucleus / GTPase activity / GTP binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koyama, M. / Shirai, N. / Matsuura, Y. | ||||||
![]() | ![]() Title: Structural insights into how yrb2p accelerates the assembly of the xpo1p nuclear export complex Authors: Koyama, M. / Shirai, N. / Matsuura, 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 | ![]() | 273.4 KB | Display | ![]() |
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PDB format | ![]() | 210.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3wyfC ![]() 3m1iS C: citing same article ( S: Starting model for refinement |
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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 ACD
#1: Protein | Mass: 20672.861 Da / Num. of mol.: 1 / Fragment: UNP residues 1-182 / Mutation: Q71L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: AWRI796 / Gene: AWRI796_3356 / Plasmid: PGEX-TEV / Production host: ![]() ![]() |
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#2: Protein | Mass: 120398.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 8022.581 Da / Num. of mol.: 1 / Mutation: S35L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 3 types, 734 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)
#4: Chemical | ChemComp-GTP / |
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#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.87 % |
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Crystal grow | pH: 7.7 Details: 0.1M TRIS, 15% PEG20000, PH 7.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 28, 2012 |
Radiation | Monochromator: ROTATED-INCLINED DOUBLE-CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→37.75 Å / Num. obs: 95343 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 4.8 % / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3M1I Resolution: 2.15→37.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.448 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.163 / 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: 31.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→37.75 Å
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