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- PDB-4y0f: Crystal Structure of Human TDP-43 RRM1 Domain in Complex with an ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4y0f | |||||||||
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Title | Crystal Structure of Human TDP-43 RRM1 Domain in Complex with an Unmodified Single-stranded DNA | |||||||||
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![]() | DNA BINDING PROTEIN/DNA / ![]() | |||||||||
Function / homology | ![]() nuclear inner membrane organization / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Chiang, C.H. / Kuo, P.H. / Doudeva, L.G. / Wang, Y.T. / Yuan, H.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation Authors: Chiang, C.H. / Grauffel, C. / Wu, L.S. / Kuo, P.H. / Doudeva, L.G. / Lim, C. / Shen, C.K. / Yuan, H.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.1 KB | Display | ![]() |
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PDB format | ![]() | 60.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4y00C ![]() 4iufS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 12064.745 Da / Num. of mol.: 2 / Fragment: UNP residues 101-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 3091.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.39 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.12M ammonium acetate, 0.08M BIS-TRIS, pH 5.5, 20% PEG 3350 PH range: 5.5-7.5 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 17, 2011 |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.648→27.701 Å / Num. all: 8322 / Num. obs: 7991 / % possible obs: 93.63 % / Redundancy: 9.7 % / Net I/σ(I): 44.43 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() ![]() Starting model: 4IUF Resolution: 2.648→27.701 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.648→27.701 Å
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Refine LS restraints |
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LS refinement shell |
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