7SQO

Structure of the orexin-2 receptor(OX2R) bound to TAK-925, Gi and scFv16


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orexin receptor type 2A [auth R]444Homo sapiensMutation(s): 0 
Gene Names: HCRTR2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O43614 (Homo sapiens)
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Go to UniProtKB:  O43614
PHAROS:  O43614
GTEx:  ENSG00000137252 
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UniProt GroupO43614
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B [auth A]354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]354Bos taurusMutation(s): 0 
Gene Names: GNB1
UniProt
Find proteins for P62871 (Bos taurus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P63212 (Bos taurus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv-16247synthetic constructMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary