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Yorodumi- PDB-5mdi: Crystal structure of TDP-43 N-terminal domain at 2.1 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mdi | ||||||
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Title | Crystal structure of TDP-43 N-terminal domain at 2.1 A resolution | ||||||
Components | TAR DNA-binding protein 43 | ||||||
Keywords | RNA BINDING PROTEIN / RNA binding proteins / Dynamic polymerization / ALS / protein aggregation | ||||||
Function / homology | Function and homology information nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / molecular condensate scaffold activity ...nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / molecular condensate scaffold activity / RNA splicing / negative regulation of protein phosphorylation / mRNA 3'-UTR binding / regulation of protein stability / regulation of circadian rhythm / positive regulation of insulin secretion / mRNA processing / cytoplasmic stress granule / positive regulation of protein import into nucleus / rhythmic process / double-stranded DNA binding / regulation of gene expression / regulation of apoptotic process / amyloid fibril formation / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / lipid binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Afroz, T. / Hock, E.-M. / Ernst, P. / Foglieni, C. / Jambeau, M. / Gilhespy, L. / Laferriere, F. / Maniecka, Z. / Plueckthun, A. / Mittl, P. ...Afroz, T. / Hock, E.-M. / Ernst, P. / Foglieni, C. / Jambeau, M. / Gilhespy, L. / Laferriere, F. / Maniecka, Z. / Plueckthun, A. / Mittl, P. / Paganetti, P. / Allain, F.H.T. / Polymenidou, M. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation. Authors: Afroz, T. / Hock, E.M. / Ernst, P. / Foglieni, C. / Jambeau, M. / Gilhespy, L.A.B. / Laferriere, F. / Maniecka, Z. / Pluckthun, A. / Mittl, P. / Paganetti, P. / Allain, F.H.T. / Polymenidou, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mdi.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mdi.ent.gz | 109.7 KB | Display | PDB format |
PDBx/mmJSON format | 5mdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/5mdi ftp://data.pdbj.org/pub/pdb/validation_reports/md/5mdi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11445.388 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TARDBP / Production host: Escherichia coli (E. coli) / References: UniProt: K7EJM5, UniProt: Q13148*PLUS #2: Chemical | ChemComp-ACT / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.13 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium cacodylate pH 6.5, 1.4 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 32038 / % possible obs: 99.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 13.13 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 10.9 % / Rmerge(I) obs: 4.95 / Mean I/σ(I) obs: 0.57 / CC1/2: 0.206 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→44.76 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.809 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.145 / 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: 47.864 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→44.76 Å
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