+Open data
-Basic information
Entry | Database: PDB / ID: 5mrg | ||||||
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Title | Solution structure of TDP-43 (residues 1-102) | ||||||
Components | TAR DNA-binding protein 43 | ||||||
Keywords | DNA BINDING PROTEIN / STRUCTURE FROM CYANA 3.97 | ||||||
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 / RNA splicing ...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 / RNA splicing / negative regulation of protein phosphorylation / molecular condensate scaffold activity / 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 / regulation of gene expression / double-stranded DNA binding / 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 | SOLUTION NMR / molecular dynamics | ||||||
Authors | Mompean, M. / Romano, V. / Pantoja-Uceda, D. / Stuani, C. / Baralle, F.E. / Laurents, D.V. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Point mutations in the N-terminal domain of transactive response DNA-binding protein 43 kDa (TDP-43) compromise its stability, dimerization, and functions. Authors: Mompean, M. / Romano, V. / Pantoja-Uceda, D. / Stuani, C. / Baralle, F.E. / Buratti, E. / Laurents, D.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mrg.cif.gz | 788.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mrg.ent.gz | 674.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mrg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mrg ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mrg | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12674.207 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-102 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TARDBP, TDP43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13148 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Sample state: isotropic / Type: 2D 1H-1H NOESY |
-Sample preparation
Details | Type: solution / Contents: 0.35 mM 13C15N TDP-43(1-102), 90% H2O/10% D2O / Label: U_13C_15N / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.35 mM / Component: TDP-43(1-102) / Isotopic labeling: 13C15N |
Sample conditions | Ionic strength: 0 Not defined / Label: conditions_1 / pH: 3.9 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz |
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-Processing
NMR software | Name: CYANA / Version: 3.97 / Developer: Guntert, Mumenthaler and Wuthrich / Classification: structure calculation |
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Refinement | Method: molecular dynamics / Software ordinal: 1 / Details: refined with AMBER |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |