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- PDB-8ejm: Crystal structure of human DEAH-box helicase DHX15 in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ejm | ||||||
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Title | Crystal structure of human DEAH-box helicase DHX15 in complex with SUGP1 G-patch | ||||||
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![]() | RNA BINDING PROTEIN / HYDROLASE / Complex / helicase / splicing factor | ||||||
Function / homology | ![]() U12-type spliceosomal complex / ATP-dependent activity, acting on RNA / response to alkaloid / antiviral innate immune response / RNA splicing / mRNA Splicing - Major Pathway / helicase activity / spliceosomal complex / response to toxic substance / mRNA processing ...U12-type spliceosomal complex / ATP-dependent activity, acting on RNA / response to alkaloid / antiviral innate immune response / RNA splicing / mRNA Splicing - Major Pathway / helicase activity / spliceosomal complex / response to toxic substance / mRNA processing / mRNA splicing, via spliceosome / double-stranded RNA binding / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / RNA helicase activity / RNA helicase / nuclear speck / defense response to bacterium / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, J. / Tong, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: DHX15 is involved in SUGP1-mediated RNA missplicing by mutant SF3B1 in cancer. Authors: Zhang, J. / Huang, J. / Xu, K. / Xing, P. / Huang, Y. / Liu, Z. / Tong, L. / Manley, J.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.8 KB | Display | ![]() |
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PDB format | ![]() | 128.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gxlC ![]() 8gxmC ![]() 6sh6S S: Starting model for refinement C: citing same article ( |
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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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 78730.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 8094.042 Da / Num. of mol.: 1 / Fragment: residues 543-614 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 6 types, 281 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ADP / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Chemical | #7: Chemical | #8: 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: 2.3 Å3/Da / Density % sol: 46.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, ammonium sulfate, HEPES buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→58.7 Å / Num. obs: 74658 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 36.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.8→1.91 Å / Rmerge(I) obs: 1.324 / Num. unique obs: 11895 / CC1/2: 0.696 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6SH6 Resolution: 1.8→58.67 Å / SU ML: 0.299 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5971 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 45.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→58.67 Å
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Refine LS restraints |
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LS refinement shell |
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