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Open data
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Basic information
Entry | Database: PDB / ID: 7byf | ||||||
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Title | The crystal structure of mouse ORF10-Rae1-Nup98 complex | ||||||
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Function / homology | ![]() Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, P. / Feng, H. | ||||||
![]() | ![]() Title: Molecular mechanism underlying selective inhibition of mRNA nuclear export by herpesvirus protein ORF10. Authors: Feng, H. / Tian, H. / Wang, Y. / Zhang, Q. / Lin, N. / Liu, S. / Yu, Y. / Deng, H. / Gao, P. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325.8 KB | Display | ![]() |
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PDB format | ![]() | 267.8 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 3 types, 6 molecules ADBEFC
#1: Protein | Mass: 39054.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q8C570 #2: Protein | Mass: 6370.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q3TPG3 #3: Protein | Mass: 46268.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GAMMAHV.ORF10, 10, ORF10 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: O41931 |
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-Non-polymers , 3 types, 449 molecules ![](data/chem/img/HG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-HG / ![]() #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.35 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M di-Sodium tartrate, 20% PEG 3350, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→48.903 Å / Num. obs: 63997 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.597 / Num. unique obs: 12416 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.16 Å2 / Biso mean: 41.4789 Å2 / Biso min: 16.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→48.903 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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