7SR8 | pdb_00007sr8

Molecular mechanism of the the wake-promoting agent TAK-925


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7SR8

This is version 1.1 of the entry. See complete history

Literature

Molecular mechanism of the wake-promoting agent TAK-925.

Yin, J.Kang, Y.McGrath, A.P.Chapman, K.Sjodt, M.Kimura, E.Okabe, A.Koike, T.Miyanohana, Y.Shimizu, Y.Rallabandi, R.Lian, P.Bai, X.Flinspach, M.De Brabander, J.K.Rosenbaum, D.M.

(2022) Nat Commun 13: 2902-2902

  • DOI: https://doi.org/10.1038/s41467-022-30601-3
  • Primary Citation Related Structures: 
    7SQO, 7SR8

  • PubMed Abstract: 

    The OX 2 orexin receptor (OX 2 R) is a highly expressed G protein-coupled receptor (GPCR) in the brain that regulates wakefulness and circadian rhythms in humans. Antagonism of OX 2 R is a proven therapeutic strategy for insomnia drugs, and agonism of OX 2 R is a potentially powerful approach for narcolepsy type 1, which is characterized by the death of orexinergic neurons. Until recently, agonism of OX 2 R had been considered 'undruggable.' We harness cryo-electron microscopy of OX 2 R-G protein complexes to determine how the first clinically tested OX 2 R agonist TAK-925 can activate OX 2 R in a highly selective manner. Two structures of TAK-925-bound OX 2 R with either a G q mimetic or G i reveal that TAK-925 binds at the same site occupied by antagonists, yet interacts with the transmembrane helices to trigger activating microswitches. Our structural and mutagenesis data show that TAK-925's selectivity is mediated by subtle differences between OX 1 and OX 2 receptor subtypes at the orthosteric pocket. Finally, differences in the polarity of interactions at the G protein binding interfaces help to rationalize OX 2 R's coupling selectivity for G q signaling. The mechanisms of TAK-925's binding, activation, and selectivity presented herein will aid in understanding the efficacy of small molecule OX 2 R agonists for narcolepsy and other circadian disorders.


  • Organizational Affiliation
    • Department of Biophysics, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.

Macromolecule Content 

  • Total Structure Weight: 150.38 kDa 
  • Atom Count: 9,083 
  • Modeled Residue Count: 1,141 
  • Deposited Residue Count: 1,326 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
a modified Guanine nucleotide-binding protein G(q) subunit alpha238Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1340Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]82Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59768
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16D [auth E]259Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypocretin receptor type 2E [auth R]407Homo sapiensMutation(s): 0 
Gene Names: HCRTR2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O43614 (Homo sapiens)
Explore O43614 
Go to UniProtKB:  O43614
PHAROS:  O43614
GTEx:  ENSG00000137252 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43614
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.1
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States5R01NS103939-03

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary