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- PDB-8a6i: Structure of the low complexity domain of TDP-43 (fragment 309-35... -

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Basic information

Entry
Database: PDB / ID: 8a6i
TitleStructure of the low complexity domain of TDP-43 (fragment 309-350) with methionine sulfoxide modifications
ComponentsTAR DNA-binding protein 43
KeywordsUNKNOWN FUNCTION / TDP-43 / low complexity domain / prion-like domain / methionine sulfoxide / LLPS
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 / positive regulation of protein import into nucleus / cytoplasmic stress granule / 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
: / TAR DNA-binding protein 43, C-terminal / TAR DNA-binding protein 43, N-terminal / TAR DNA-binding protein 43, N-terminal domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
TAR DNA-binding protein 43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / na
AuthorsCarrasco, J. / Anton, R. / Pantoja-Uceda, D. / Laurents, D.V. / Oroz, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-109276RA-I00/AEI/10.13039/501100011033 Spain
CitationJournal: Nat Commun / Year: 2023
Title: Metamorphism in TDP-43 prion-like domain determines chaperone recognition.
Authors: Carrasco, J. / Anton, R. / Valbuena, A. / Pantoja-Uceda, D. / Mukhi, M. / Hervas, R. / Laurents, D.V. / Gasset, M. / Oroz, J.
History
DepositionJun 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAR DNA-binding protein 43


Theoretical massNumber of molelcules
Total (without water)4,3321
Polymers4,3321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide TAR DNA-binding protein 43 / TDP-43


Mass: 4331.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARDBP, TDP43 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q13148
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
214isotropic12D 1H-15N HSQC
224isotropic13D HNCO
234isotropic13D HN(CA)CO
244isotropic13D HNCA
254isotropic13D CBCA(CO)NH
264isotropic13D HCC(CO)NH
274isotropic13D HNNH
284isotropic13D HNHA
294isotropic13D 1H-15N NOESY
2104isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

DetailsType: solution
Contents: 500 uM [U-13C; U-15N] TDP-43 fragment 309-350, 20 mM HEPES, 10 mM potassium chloride, 5 mM MgCl2, 1 mM ATP, 90% H2O/10% D2O
Label: 15N/13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMTDP-43 fragment 309-350[U-13C; U-15N]4
20 mMHEPESnatural abundance4
10 mMpotassium chloridenatural abundance4
5 mMMgCl2natural abundance4
1 mMATPnatural abundance4
Sample conditionsIonic strength: 10 mM / Ionic strength err: 0.05 / Label: conditions_4 / pH: 6.8 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 288 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
Sparky3.19Goddardchemical shift assignment
TopSpin4.0.8Bruker Biospinprocessing
RefinementMethod: na / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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