5MO9

Structure of human TrkB receptor ligand binding domain in complex with the Fab frgment of antibody AB20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.594 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Pharmaceutical Characterization of Tropomyosin Receptor Kinase B-Agonistic Antibodies on Human Induced Pluripotent Stem (hiPS) Cell-Derived Neurons.

Traub, S.Stahl, H.Rosenbrock, H.Simon, E.Florin, L.Hospach, L.Horer, S.Heilker, R.

(2017) J. Pharmacol. Exp. Ther. 361: 355-365

  • DOI: 10.1124/jpet.117.240184

  • PubMed Abstract: 
  • Brain-derived neurotrophic factor (BDNF) is a central modulator of neuronal development and synaptic plasticity in the central nervous system. This renders the BDNF-modulated tropomyosin receptor kinase B (TrkB) a promising drug target to treat synap ...

    Brain-derived neurotrophic factor (BDNF) is a central modulator of neuronal development and synaptic plasticity in the central nervous system. This renders the BDNF-modulated tropomyosin receptor kinase B (TrkB) a promising drug target to treat synaptic dysfunctions. Using GRowth factor-driven expansion and INhibition of NotCH (GRINCH) during maturation, the so-called GRINCH neurons were derived from human-induced pluripotent stem cells. These GRINCH neurons were used as model cells for pharmacologic profiling of two TrkB-agonistic antibodies, hereafter referred to as AB2 and AB20 In next-generation sequencing studies, AB2 and AB20 stimulated transcriptional changes, which extensively overlapped with BDNF-driven transcriptional modulation. In regard to TrkB phosphorylation, both AB2 and AB20 were only about half as efficacious as BDNF; however, with respect to the TrkB downstream signaling, AB2 and AB20 displayed increased efficacy values, providing a stimulation at least comparable to BDNF in respect to VGF transcription, as well as of AKT and cAMP response element-binding protein phosphorylation. In a complex structure of the TrkB-d5 domain with AB20, determined by X-ray crystallography, the AB20 binding site was found to be allosteric in regard to the BDNF binding site, whereas AB2 was known to act orthosterically with BDNF. In agreement with this finding, AB2 and AB20 acted synergistically at greater concentrations to drive TrkB phosphorylation. Although TrkB downstream signaling declined faster after pulse stimulation with AB20 than with AB2, AB20 restimulated TrkB phosphorylation more efficiently than AB2. In conclusion, both antibodies displayed some limitations and some benefits in regard to future applications as therapeutic agents.


    Organizational Affiliation

    Trenzyme GmbH, Konstanz (S.T.) Germany, Lead Identification and Optimization Support (L.H., S.H., R.H.), Immunological and Respiratory Diseases Research (H.S.), CNS Diseases Research (H.R.), and Target Discovery Research (E.S.), Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany; and Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut (L.F.).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AB20 Fab heavy chain
H
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AB20 Fab light chain
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BDNF/NT-3 growth factors receptor
X
151Homo sapiensMutation(s): 0 
Gene Names: NTRK2 (TRKB)
EC: 2.7.10.1
Find proteins for Q16620 (Homo sapiens)
Go to Gene View: NTRK2
Go to UniProtKB:  Q16620
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.594 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 148.370α = 90.00
b = 55.430β = 90.00
c = 69.390γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-12-14 
  • Released Date: 2017-08-02 
  • Deposition Author(s): Hoerer, S.

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release