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- PDB-5x4f: Solution Structure of the N-terminal Domain of TDP-43 -

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Basic information

Entry
Database: PDB / ID: 5x4f
TitleSolution Structure of the N-terminal Domain of TDP-43
ComponentsTAR DNA-binding protein 43
KeywordsDNA BINDING PROTEIN / Dimerization
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
: / 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 / molecular dynamics
AuthorsJiang, L.-L. / Xue, W. / Hu, H.-Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31200570 China
CitationJournal: Sci Rep / Year: 2017
Title: The N-terminal dimerization is required for TDP-43 splicing activity.
Authors: Jiang, L.L. / Xue, W. / Hong, J.Y. / Zhang, J.T. / Li, M.J. / Yu, S.N. / He, J.H. / Hu, H.Y.
History
DepositionFeb 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
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
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)8,5021
Polymers8,5021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4980 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 8502.391 Da / Num. of mol.: 1 / Fragment: UNP residues 1-77 / Mutation: C39S/C50S
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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D HNHA
191isotropic13D 1H-15N NOESY
181isotropic13D (H)CCH-TOCSY
171isotropic13D C(CO)NH
161isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

DetailsType: solution
Contents: 1 mM U-99% 13C; U-99% 15N TDP(1-77)-GB1-C39/C50S, 20 mM sodium phosphate, 50 mM sodium chloride, 0.05 v/v sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O
Label: 15N,13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTDP(1-77)-GB1-C39/C50S[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.05 v/vsodium azidenatural abundance1
90 %H2Onatural abundance1
10 %D2Onatural abundance1
Sample conditionsIonic strength: 0.08 M / Label: conditons_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIALinge, O'Donoghue and Nilgesstructure calculation
MOLMOLKoradi, Billeter and Wuthrichstructure calculation
TopSpinBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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