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- PDB-2n4g: Solution Structure of the G335D Mutant of TDP-43 Amyloidogenic Co... -

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Basic information

Entry
Database: PDB / ID: 2n4g
TitleSolution Structure of the G335D Mutant of TDP-43 Amyloidogenic Core Region
ComponentsTAR DNA-binding protein 43
KeywordsDNA BINDING PROTEIN / TDP-43 / Amyloidogenic Core Region / G335D
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 / molecular dynamics
Model detailslowest energy, model1
AuthorsJiang, L. / Zhao, J. / Hu, H.
CitationJournal: Sci Rep / Year: 2016
Title: Two mutations G335D and Q343R within the amyloidogenic core region of TDP-43 influence its aggregation and inclusion formation
Authors: Jiang, L.L. / Zhao, J. / Yin, X.F. / He, W.T. / Yang, H. / Che, M.X. / Hu, H.Y.
History
DepositionJun 17, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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)5,2661
Polymers5,2661
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 5265.833 Da / Num. of mol.: 1 / Fragment: UNP residues 311-360
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
Sequence detailsG335D IS NATURAL VARIENT ACCORDING TO DATABASE Q13148 (TADBP_HUMAN).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNHA
1513D C(CO)NH
1613D 1H-13C NOESY aliphatic
1713D 1H-15N NOESY
1813D HNCO
1913D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 600 uM [U-99% 13C; U-99% 15N] GB1-TDP(311-360)-G335D-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 8 % [U-99% 2H] D2O-4, 0.02 w/v sodium azide-5, 92 % H2O-6, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMGB1-TDP(311-360)-G335D-1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
8 %D2O-4[U-99% 2H]1
0.02 w/vsodium azide-51
92 %H2O-61
Sample conditionsIonic strength: 80 / pH: 6.5 / Pressure: ambient / 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 solution
ARIALinge, O'Donoghue and Nilgesstructure solution
MOLMOLKoradi, Billeter and Wuthrichstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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