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- PDB-4bs2: NMR structure of human TDP-43 tandem RRMs in complex with UG-rich RNA -

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Basic information

Entry
Database: PDB / ID: 4bs2
TitleNMR structure of human TDP-43 tandem RRMs in complex with UG-rich RNA
Components
  • 5'-R(*GP*UP*GP*UP*GP*AP*AP*UP*GP*AP*AP*UP)-3'
  • TAR DNA-BINDING PROTEIN 43
KeywordsTRANSCRIPTION / HNRNP / CYSTIC FIBROSIS / NEURODEGENERATION / ISOTOPE-LABELLED RNA / HAMMERHEAD RIBOZYME
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 / molecular condensate scaffold activity / response to endoplasmic reticulum stress ...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 / molecular condensate scaffold activity / response to endoplasmic reticulum stress / 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 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...: / TAR DNA-binding protein 43, C-terminal / TAR DNA-binding protein 43, N-terminal / TAR DNA-binding protein 43, N-terminal domain / RRM (RNA recognition motif) 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / TAR DNA-binding protein 43
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS IN TORSION ANGLE SPACE
AuthorsLukavsky, P.J. / Daujotyte, D. / Tollervey, J.R. / Ule, J. / Stuani, C. / Buratti, E. / Baralle, F.E. / Damberger, F.F. / Allain, F.H.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Molecular Basis of Ug-Rich RNA Recognition by the Human Splicing Factor Tdp-43
Authors: Lukavsky, P.J. / Daujotyte, D. / Tollervey, J.R. / Ule, J. / Stuani, C. / Buratti, E. / Baralle, F.E. / Damberger, F.F. / Allain, F.H.T.
History
DepositionJun 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Dec 18, 2013Group: Database references
Revision 1.4May 4, 2016Group: Atomic model / Other
Revision 1.5Jun 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_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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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
B: 5'-R(*GP*UP*GP*UP*GP*AP*AP*UP*GP*AP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)23,8732
Polymers23,8732
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50LOWEST ENERGY AND RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein TAR DNA-BINDING PROTEIN 43 / / TDP-43 / TDP-43 TANDEM RRMS


Mass: 19995.734 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN, RESIDUES 102-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q13148
#2: RNA chain 5'-R(*GP*UP*GP*UP*GP*AP*AP*UP*GP*AP*AP*UP)-3' / UG-RICH RNA


Mass: 3877.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D C13-EDITED NOESY
1213D N15- EDITED NOESY
1312D NOESY
1412D TOCSY
1513D (H)CCH-TOCSY
NMR detailsText: MEASUREMENTS WERE PERFORMED ON THREE DIFFERENT SAMPLES,15N -LABELLED TDP-43 WITH UNLABELLED RNA, 13C,15N- LABELLED TDP-43 WITH UNLABELLED RNA, 15N-LABELLED TDP-43 WITH 13C,15N-LABELLED RNA

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Sample preparation

DetailsContents: 94%WATER/6%D2O
Sample conditionsIonic strength: 50 mM / pH: 6.8 / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCASE ET ALrefinement
CYANAstructure solution
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS IN TORSION ANGLE SPACE
Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY AND RESTRAINT VIOLATION
Conformers calculated total number: 50 / Conformers submitted total number: 20

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