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- PDB-6b1g: Solution structure of TDP-43 N-terminal domain dimer. -

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Basic information

Entry
Database: PDB / ID: 6b1g
TitleSolution structure of TDP-43 N-terminal domain dimer.
Components
  • TAR DNA-binding protein 43, S48E Mutant
  • TAR DNA-binding protein 43, Y4R Mutant
KeywordsSTRUCTURAL PROTEIN / TDP-43 / Amyotrophic Lateral Sclerosis / Protein Aggregation / RNA binding protein / Protein self-assembly / 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 / 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 / simulated annealing
AuthorsNaik, M.T. / Wang, A. / Conicella, A. / Fawzi, N.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118530 United States
ALS Association17-IIP-342 United States
CitationJournal: EMBO J. / Year: 2018
Title: A single N-terminal phosphomimic disrupts TDP-43 polymerization, phase separation, and RNA splicing.
Authors: Wang, A. / Conicella, A.E. / Schmidt, H.B. / Martin, E.W. / Rhoads, S.N. / Reeb, A.N. / Nourse, A. / Ramirez Montero, D. / Ryan, V.H. / Rohatgi, R. / Shewmaker, F. / Naik, M.T. / Mittag, T. ...Authors: Wang, A. / Conicella, A.E. / Schmidt, H.B. / Martin, E.W. / Rhoads, S.N. / Reeb, A.N. / Nourse, A. / Ramirez Montero, D. / Ryan, V.H. / Rohatgi, R. / Shewmaker, F. / Naik, M.T. / Mittag, T. / Ayala, Y.M. / Fawzi, N.L.
History
DepositionSep 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAR DNA-binding protein 43, S48E Mutant
B: TAR DNA-binding protein 43, Y4R Mutant


Theoretical massNumber of molelcules
Total (without water)18,4412
Polymers18,4412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Please see our paper for additional details.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1490 Å2
ΔGint-6 kcal/mol
Surface area9140 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TAR DNA-binding protein 43, S48E Mutant / TDP-43


Mass: 9244.335 Da / Num. of mol.: 1 / Fragment: NTD domain / Mutation: S48E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARDBP, TDP43 / Plasmid: pJ411/TDP-43 S48E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13148
#2: Protein TAR DNA-binding protein 43, Y4R Mutant / TDP-43


Mass: 9196.318 Da / Num. of mol.: 1 / Fragment: NTD domain / Mutation: Y4R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARDBP, TDP43 / Plasmid: pJ411/TDP-43 Y4R / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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
122isotropic12D 1H-15N HSQC
131isotropic12D 1H-13C HSQC
142isotropic12D 1H-13C HSQC
151isotropic23D HNCO
1222isotropic23D HNCO
1211isotropic23D HNCA
1202isotropic23D HNCA
1191isotropic23D CBCA(CO)NH
1182isotropic23D CBCA(CO)NH
1171isotropic23D HBHA(CO)NH
1162isotropic23D HBHA(CO)NH
1151isotropic23D (H)CCH-COSY
1242isotropic23D CCH-TOCSY
1231isotropic23D CCH-TOCSY
1142isotropic23D (H)CCH-COSY
1131isotropic2(HB)CB(CGCD)HD
1122isotropic2(HB)CB(CGCD)HD
1111isotropic2(HB)CB(CGCDCE)HE
1102isotropic2(HB)CB(CGCDCE)HE
191isotropic13D 1H-13C NOESY aliphatic
1272isotropic13D 1H-13C NOESY aliphatic
1261isotropic13D 1H-13C NOESY aromatic
1252isotropic13D 1H-13C NOESY aromatic
181isotropic13D 1H-15N NOESY
172isotropic13D 1H-15N NOESY
161isotropic23D Filtered 1H-13C NOESY
1292isotropic23D Filtered 1H-13C NOESY
1281isotropic23D Filtered 1H-15N NOESY
1302isotropic23D Filtered 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.7 mM [U-99% 13C; U-99% 15N] TDP-43 NTD S48E, 2.0 mM TDP-43 NTD Y4R, 20 mM HEPES, 1 mM DTT, 90% H2O/10% D2O13C, 15N- S48E + Unlabeled Y4R (1:3)S48E Complex90% H2O/10% D2O
solution20.7 mM [U-99% 13C; U-99% 15N] TDP-43 NTD Y4R, 2 mM TDP-43 NTD S48E, 20 mM HEPES, 1 mM DTT, 90% H2O/10% D2O13C, 15N- Y4R + Unlabeled S48E (1:3)Y4R Complex90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMTDP-43 NTD S48E[U-99% 13C; U-99% 15N]1
2.0 mMTDP-43 NTD Y4Rnatural abundance1
20 mMHEPESnatural abundance1
1 mMDTTnatural abundance1
0.7 mMTDP-43 NTD Y4R[U-99% 13C; U-99% 15N]2
2 mMTDP-43 NTD S48Enatural abundance2
20 mMHEPESnatural abundance2
1 mMDTTnatural abundance2
Sample conditionsDetails: Data acquired in 5mm NMR tubes. / Ionic strength: 0 mM / Ionic strength err: 0.01 / Label: Condition 1 / pH: 6.8 / PH err: 0.01 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD8501TCI HCN z-gradient cryoprobe
Bruker AVANCE IIBrukerAVANCE II5002TCI HCN z-gradient cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.45Schwieters, Kuszewski, Tjandra and Clorerefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddardpeak picking
TopSpin3.5Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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