DD homodimer

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural basis of death domain signaling in the p75 neurotrophin receptor

Lin, Z.Tann, J.Y.Goh, E.T.Kelly, C.Lim, K.B.Gao, J.F.Ibanez, C.F.

(2015) Elife 4: 11692-11692

  • DOI: https://doi.org/10.7554/eLife.11692
  • Primary Citation of Related Structures:  
    2N7Z, 2N80, 2N83, 2N97

  • PubMed Abstract: 

    Death domains (DDs) mediate assembly of oligomeric complexes for activation of downstream signaling pathways through incompletely understood mechanisms. Here we report structures of complexes formed by the DD of p75 neurotrophin receptor (p75(NTR)) with RhoGDI, for activation of the RhoA pathway, with caspase recruitment domain (CARD) of RIP2 kinase, for activation of the NF-kB pathway, and with itself, revealing how DD dimerization controls access of intracellular effectors to the receptor. RIP2 CARD and RhoGDI bind to p75(NTR) DD at partially overlapping epitopes with over 100-fold difference in affinity, revealing the mechanism by which RIP2 recruitment displaces RhoGDI upon ligand binding. The p75(NTR) DD forms non-covalent, low-affinity symmetric dimers in solution. The dimer interface overlaps with RIP2 CARD but not RhoGDI binding sites, supporting a model of receptor activation triggered by separation of DDs. These structures reveal how competitive protein-protein interactions orchestrate the hierarchical activation of downstream pathways in non-catalytic receptors.

  • Organizational Affiliation

    Department of Physiology, National University of Singapore, Singapore, Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 16
A, B
98Homo sapiensMutation(s): 0 
Gene Names: NGFRTNFRSF16
UniProt & NIH Common Fund Data Resources
Find proteins for P08138 (Homo sapiens)
Explore P08138 
Go to UniProtKB:  P08138
PHAROS:  P08138
GTEx:  ENSG00000064300 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08138
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Structure summary
  • Version 1.2: 2023-06-14
    Changes: Data collection, Database references, Other