8DPX

Preligand association structure of DR5

  • Classification: APOPTOSIS
  • Organism(s): Homo sapiens
  • Expression System: Komagataella pastoris
  • Mutation(s): No 

  • Deposited: 2022-07-17 Released: 2023-02-15 
  • Deposition Author(s): Du, G., Zhao, L., Chou, J.J.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Autoinhibitory structure of preligand association state implicates a new strategy to attain effective DR5 receptor activation.

Du, G.Zhao, L.Zheng, Y.Belfetmi, A.Cai, T.Xu, B.Heyninck, K.Van Den Heede, K.Buyse, M.A.Fontana, P.Bowman, M.Lin, L.L.Wu, H.Chou, J.J.

(2023) Cell Res 33: 131-146

  • DOI: https://doi.org/10.1038/s41422-022-00755-2
  • Primary Citation of Related Structures:  
    8DPX

  • PubMed Abstract: 

    Members of the tumor necrosis factor receptor superfamily (TNFRSF) are important therapeutic targets that can be activated to induce death of cancer cells or stimulate proliferation of immune cells. Although it has long been implicated that these receptors assemble preligand associated states that are required for dominant interference in human disease, such states have so far eluded structural characterization. Here, we find that the ectodomain of death receptor 5 (DR5-ECD), a representative member of TNFRSF, can specifically self-associate when anchored to lipid bilayer, and we report this self-association structure determined by nuclear magnetic resonance (NMR). Unexpectedly, two non-overlapping interaction interfaces are identified that could propagate to higher-order clusters. Structure-guided mutagenesis indicates that the observed preligand association structure is represented on DR5-expressing cells. The DR5 preligand association serves an autoinhibitory role as single-domain antibodies (sdAbs) that partially dissociate the preligand cluster can sensitize the receptor to its ligand TRAIL and even induce substantial receptor signaling in the absence of TRAIL. Unlike most agonistic antibodies that require multivalent binding to aggregate receptors for activation, these agonistic sdAbs are monovalent and act specifically on an oligomeric, autoinhibitory configuration of the receptor. Our data indicate that receptors such as DR5 can form structurally defined preclusters incompatible with signaling and that true agonists should disrupt the preligand cluster while converting it to signaling-productive cluster. This mechanism enhances our understanding of a long-standing question in TNFRSF signaling and suggests a new opportunity for developing agonistic molecules by targeting receptor preligand clustering.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 10B
A, B, C
109Homo sapiensMutation(s): 0 
Gene Names: TNFRSF10BDR5KILLERTRAILR2TRICK2ZTNFR9UNQ160/PRO186
UniProt & NIH Common Fund Data Resources
Find proteins for O14763 (Homo sapiens)
Explore O14763 
Go to UniProtKB:  O14763
PHAROS:  O14763
GTEx:  ENSG00000120889 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14763
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • 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 Allergy and Infectious Diseases (NIH/NIAID)United StatesAI150709
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140887

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release