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- PDB-2n4p: Solution structure of the n-terminal domain of tdp-43 -

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Basic information

Entry
Database: PDB / ID: 2n4p
TitleSolution structure of the n-terminal domain of tdp-43
ComponentsTAR DNA-binding protein 43
KeywordsDNA BINDING PROTEIN
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
: / 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 / ENERGY MINIMIZATION
Model detailslowest energy, model1
AuthorsMompean, M. / Romano, V. / Pantoja-Uceda, D. / Stuani, C. / Baralle, F. / Buratti, E. / Laurents, D.V.
CitationJournal: Febs J. / Year: 2016
Title: The TDP-43 N-terminal domain structure at high resolution.
Authors: Mompean, M. / Romano, V. / Pantoja-Uceda, D. / Stuani, C. / Baralle, F.E. / Buratti, E. / Laurents, D.V.
History
DepositionJun 26, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)9,8541
Polymers9,8541
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 9853.936 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-77
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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CO)CA
1713D CBCA(CO)NH
1813D HBHA(CO)NH
1913D HN(CO)CA
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY aliphatic
11212D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.5-0.7 mM [U-13C; U-15N] NTD, TCEP, CD3COOD/ CD3COO-Na+, NaN3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM
Component: NTD ; TCEP ; D2O ; CD3COOD/ CD3COO-Na+ ; H2O ; NaN3-1
Isotopic labeling: [U-13C; U-15N] / Conc. range: 0.5-0.7
Sample conditionspH: 3.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: ENERGY MINIMIZATION / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 30 / Protein psi angle constraints total count: 30
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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