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- EMDB-61798: Cryo-EM structure of PTH-PTH1R-Gq complex (tilted state; focused ... -

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Basic information

Entry
Database: EMDB / ID: EMD-61798
TitleCryo-EM structure of PTH-PTH1R-Gq complex (tilted state; focused refinement map)
Map data
Sample
  • Complex: PTH-PTH1R-Gq complex
KeywordsClass B GPCRs / Gq / PTH / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsSano FK / Hirano H / Itoh Y / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Chem Biol / Year: 2025
Title: Insights into G-protein coupling preference from cryo-EM structures of G-bound PTH1R.
Authors: Fumiya K Sano / Kota Shimizume / Kazuhiro Kobayashi / Toshikuni Awazu / Kouki Kawakami / Hiroaki Akasaka / Takaaki A Kobayashi / Tatsuki Tanaka / Hiroyuki H Okamoto / Hisato Hirano / Tsukasa ...Authors: Fumiya K Sano / Kota Shimizume / Kazuhiro Kobayashi / Toshikuni Awazu / Kouki Kawakami / Hiroaki Akasaka / Takaaki A Kobayashi / Tatsuki Tanaka / Hiroyuki H Okamoto / Hisato Hirano / Tsukasa Kusakizako / Wataru Shihoya / Yoshiaki Kise / Yuzuru Itoh / Ryuichiro Ishitani / Yasushi Okada / Yasushi Sako / Masataka Yanagawa / Asuka Inoue / Osamu Nureki /
Abstract: The parathyroid hormone type 1 receptor (PTH1R) is a prototypical class B1 G-protein-coupled receptor that couples to both G and G, having a crucial role in calcium homeostasis and serving as a ...The parathyroid hormone type 1 receptor (PTH1R) is a prototypical class B1 G-protein-coupled receptor that couples to both G and G, having a crucial role in calcium homeostasis and serving as a therapeutic target for osteoporosis. Therapies targeting PTH1R face challenges because of G-associated prolonged signaling, which leads to bone resorption. To address this, selective activation of G signaling is desirable. However, the structural basis of G-mediated signaling remains unclear, limiting the development of signal-selective drugs. Here, we present cryo-electron microscopy structures of the PTH1R-G complex in two distinct extracellular conformations, demonstrating the role of N-linked glycans at N176 in stabilizing the ligand-tilted conformation. Comparison with a G-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 signaling. These structural insights provide a foundation for understanding the molecular mechanisms of PTH1R signaling.
History
DepositionOct 4, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61798.png

Downloads & links

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Map

FileDownload / File: emd_61798.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 260 pix.
= 265.2 Å		1.02 Å/pix.
x 260 pix.
= 265.2 Å		1.02 Å/pix.
x 260 pix.
= 265.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.49340913 - 1.0623151
Average (Standard dev.)-0.00067714497 (±0.02108015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 265.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61798_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_61798_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61798_half_map_2.map
Projections & Slices
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Sample components

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Entire : PTH-PTH1R-Gq complex

EntireName: PTH-PTH1R-Gq complex
Components
  • Complex: PTH-PTH1R-Gq complex

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Supramolecule #1: PTH-PTH1R-Gq complex

SupramoleculeName: PTH-PTH1R-Gq complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 259479
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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