8OYD | pdb_00008oyd

TrkB transmembrane domain NMR structure in DMPC/DHPC bicelles


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the transmembrane signaling and antidepressant-induced activation of the receptor tyrosine kinase TrkB.

Kot, E.F.Goncharuk, S.A.Franco, M.L.McKenzie, D.M.Arseniev, A.S.Benito-Martinez, A.Costa, M.Cattaneo, A.Hristova, K.Vilar, M.Mineev, K.S.

(2024) Nat Commun 15: 9316-9316

  • DOI: https://doi.org/10.1038/s41467-024-53710-7
  • Primary Citation of Related Structures:  
    8OYD

  • PubMed Abstract: 

    Neurotrophin receptors of the Trk family are involved in the regulation of brain development and neuroplasticity, and therefore can serve as targets for anti-cancer and stroke-recovery drugs, antidepressants, and many others. The structures of Trk protein domains in various states upon activation need to be elucidated to allow rational drug design. However, little is known about the conformations of the transmembrane and juxtamembrane domains of Trk receptors. In the present study, we employ NMR spectroscopy to solve the structure of the TrkB dimeric transmembrane domain in the lipid environment. We verify the structure using mutagenesis and confirm that the conformation corresponds to the active state of the receptor. Subsequent study of TrkB interaction with the antidepressant drug fluoxetine, and the antipsychotic drug chlorpromazine, provides a clear self-consistent model, describing the mechanism by which fluoxetine activates the receptor by binding to its transmembrane domain.


  • Organizational Affiliation
    • Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BDNF/NT-3 growth factors receptor
A, B
45Homo sapiensMutation(s): 0 
Gene Names: NTRK2TRKB
EC: 2.7.10.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16620 (Homo sapiens)
Explore Q16620 
Go to UniProtKB:  Q16620
PHAROS:  Q16620
GTEx:  ENSG00000148053 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16620
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation22-14-00130

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Database references, Structure summary
  • Version 1.2: 2024-11-13
    Changes: Database references