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 9JR2 | pdb_00009jr2

Cryo-EM structure of PTH-PTH1R-Gq (upright state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9JR2

This is version 1.4 of the entry. See complete history. 

Literature

Insights into G-protein coupling preference from cryo-EM structures of G q -bound PTH1R.

Sano, F.K., Shimizume, K., Kobayashi, K., Awazu, T., Kawakami, K., Akasaka, H., Kobayashi, T.A., Tanaka, T., Okamoto, H.H., Hirano, H., Kusakizako, T., Shihoya, W., Kise, Y., Itoh, Y., Ishitani, R., Okada, Y., Sako, Y., Yanagawa, M., Inoue, A., Nureki, O.

(2025) Nat Chem Biol 21: 1906-1914

  • DOI: https://doi.org/10.1038/s41589-025-01957-6
  • Primary Citation Related Structures: 
    9JR2, 9JR3

  • PubMed Abstract: 

    The parathyroid hormone type 1 receptor (PTH1R) is a prototypical class B1 G-protein-coupled receptor that couples to both G q and G s , having a crucial role in calcium homeostasis and serving as a therapeutic target for osteoporosis. Therapies targeting PTH1R face challenges because of G q -associated prolonged signaling, which leads to bone resorption. To address this, selective activation of G s signaling is desirable. However, the structural basis of G q -mediated signaling remains unclear, limiting the development of signal-selective drugs. Here, we present cryo-electron microscopy structures of the PTH1R-G q complex in two distinct extracellular conformations, demonstrating the role of N-linked glycans at N176 1.28 in stabilizing the ligand-tilted conformation. Comparison with a G s -bound PTH1R structure highlights the role of key interactions involving both the C terminus of Gα and the receptor's intracellular loop 2 in G q signaling. These structural insights provide a foundation for understanding the molecular mechanisms of PTH1R signaling.


  • Organizational Affiliation: 
    • Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 168.86 kDa 
  • Atom Count: 9,418 
  • Modeled Residue Count: 1,226 
  • Deposited Residue Count: 1,518 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(q) subunit alpha-1 (miniGq)245Homo sapiensMutation(s): 0 
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
Entity Groups
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UniProt GroupP63092
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1344Rattus rattusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
Explore P54311 
Go to UniProtKB:  P54311
Entity Groups
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UniProt GroupP54311
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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]67Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt
Find proteins for P63212 (Bos taurus)
Explore P63212 
Go to UniProtKB:  P63212
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UniProt GroupP63212
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16D [auth S]260Mus musculusMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Parathyroid hormoneE [auth P]35Homo sapiensMutation(s): 1 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P01270 (Homo sapiens)
Explore P01270 
Go to UniProtKB:  P01270
PHAROS:  P01270
GTEx:  ENSG00000152266 
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UniProt GroupP01270
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Parathyroid hormone/parathyroid hormone-related peptide receptorF [auth R]567Homo sapiensMutation(s): 0 
Gene Names: PTH1R, PTHR, PTHR1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03431 (Homo sapiens)
Explore Q03431 
Go to UniProtKB:  Q03431
PHAROS:  Q03431
GTEx:  ENSG00000160801 
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UniProt GroupQ03431
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection
  • Version 1.2: 2025-07-02
    Changes: Data collection
  • Version 1.3: 2025-07-09
    Changes: Data collection, Database references
  • Version 1.4: 2025-12-10
    Changes: Data collection, Database references