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Yorodumi- PDB-3d2w: Crystal structure of mouse TDP-43 RRM2 domain in complex with DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d2w | ||||||
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Title | Crystal structure of mouse TDP-43 RRM2 domain in complex with DNA | ||||||
Components |
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Keywords | DNA/RNA BINDING PROTEIN / DP-43 proteinopathy / TDP-43 inclusions / RNA recognition motif / FTLD-U / ALS / RRM / DNA-RNA BINDING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information nuclear inner membrane organization / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / negative regulation by host of viral transcription / pre-mRNA intronic binding / RNA splicing / negative regulation of protein phosphorylation / mRNA 3'-UTR binding / regulation of protein stability / regulation of circadian rhythm ...nuclear inner membrane organization / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / negative regulation by host of viral transcription / pre-mRNA intronic binding / RNA splicing / negative regulation of protein phosphorylation / mRNA 3'-UTR binding / regulation of protein stability / regulation of circadian rhythm / mRNA processing / cytoplasmic stress granule / positive regulation of protein import into nucleus / rhythmic process / gene expression / double-stranded DNA binding / regulation of apoptotic process / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Kuo, P.H. / Yuan, H.S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2009 Title: Structural insights into TDP-43 in nucleic-acid binding and domain interactions Authors: Kuo, P.H. / Doudeva, L.G. / Wang, Y.T. / Shen, C.K. / Yuan, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d2w.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d2w.ent.gz | 23 KB | Display | PDB format |
PDBx/mmJSON format | 3d2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/3d2w ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d2w | HTTPS FTP |
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-Related structure data
Related structure data | 1wf0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10097.466 Da / Num. of mol.: 1 / Fragment: RRM2 motif, UNP residues 192-265 Source method: isolated from a genetically manipulated source Details: brain / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tardbp, Tdp43 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q921F2 |
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#2: DNA chain | Mass: 3091.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.54 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: Reservoir solution containing 2M (NH4)2SO4, 0.1M phosphate-citrate, the reservoir solution contained an addition of 10% glycerol, pH4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 23, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→25.46 Å / Num. all: 13674 / Num. obs: 13854 / % possible obs: 98.7 % / Observed criterion σ(F): 1.87 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.51 / Num. unique all: 1310 / Rsym value: 0.32 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WF0 Resolution: 1.65→25.46 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.912 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.109 / 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: 23.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.201 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→25.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.651→1.694 Å / Rfactor Rfree error: 0.11 / Total num. of bins used: 20
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