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 6B1G | pdb_00006b1g

Solution structure of TDP-43 N-terminal domain dimer.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 6B1G

This is version 1.3 of the entry. See complete history. 

Literature

A single N-terminal phosphomimic disrupts TDP-43 polymerization, phase separation, and RNA splicing.

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.

(2018) EMBO J 37

  • DOI: https://doi.org/10.15252/embj.201797452
  • Primary Citation Related Structures: 
    6B1G

  • PubMed Abstract: 

    TDP-43 is an RNA-binding protein active in splicing that concentrates into membraneless ribonucleoprotein granules and forms aggregates in amyotrophic lateral sclerosis (ALS) and Alzheimer's disease. Although best known for its predominantly disordered C-terminal domain which mediates ALS inclusions, TDP-43 has a globular N-terminal domain (NTD). Here, we show that TDP-43 NTD assembles into head-to-tail linear chains and that phosphomimetic substitution at S48 disrupts TDP-43 polymeric assembly, discourages liquid-liquid phase separation (LLPS) in vitro , fluidizes liquid-liquid phase separated nuclear TDP-43 reporter constructs in cells, and disrupts RNA splicing activity. Finally, we present the solution NMR structure of a head-to-tail NTD dimer comprised of two engineered variants that allow saturation of the native polymerization interface while disrupting higher-order polymerization. These data provide structural detail for the established mechanistic role of the well-folded TDP-43 NTD in splicing and link this function to LLPS. In addition, the fusion-tag solubilized, recombinant form of TDP-43 full-length protein developed here will enable future phase separation and in vitro biochemical assays on TDP-43 function and interactions that have been hampered in the past by TDP-43 aggregation.


  • Organizational Affiliation: 
    • Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA.

Macromolecule Content 

  • Total Structure Weight: 18.44 kDa 
  • Atom Count: 1,246 
  • Modeled Residue Count: 160 
  • Deposited Residue Count: 166 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TAR DNA-binding protein 43, S48E Mutant83Homo sapiensMutation(s): 1 
Gene Names: TARDBP, TDP43
UniProt & NIH Common Fund Data Resources
Find proteins for Q13148 (Homo sapiens)
Explore Q13148 
Go to UniProtKB:  Q13148
PHAROS:  Q13148
GTEx:  ENSG00000120948 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13148
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TAR DNA-binding protein 43, Y4R Mutant83Homo sapiensMutation(s): 1 
Gene Names: TARDBP, TDP43
UniProt & NIH Common Fund Data Resources
Find proteins for Q13148 (Homo sapiens)
Explore Q13148 
Go to UniProtKB:  Q13148
PHAROS:  Q13148
GTEx:  ENSG00000120948 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13148
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM118530
ALS AssociationUnited States17-IIP-342

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references