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- EMDB-70374: Structure of the MOR/Gi/DAMGO Complex, GTP-Bound, G-ACT-2/3 Conse... -

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Basic information

Entry
Database: EMDB / ID: EMD-70374
TitleStructure of the MOR/Gi/DAMGO Complex, GTP-Bound, G-ACT-2/3 Consensus Refinement
Map data
Sample
  • Complex: Mu Opioid Receptor Gi1 heterotrimer complex
KeywordsGPCR / Complex / Agonist / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsRobertson MJ / Skiniotis G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)HD107581 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR230042 United States
CitationJournal: Nature / Year: 2025
Title: Non-equilibrium snapshots of ligand efficacy at the μ-opioid receptor.
Authors: Michael J Robertson / Arnab Modak / Makaía M Papasergi-Scott / Miaohui Hu / Maria Claudia Peroto / Balazs R Varga / Susruta Majumdar / Ravi Kalathur / Scott C Blanchard / Georgios Skiniotis /
Abstract: Distinct ligands for the same G-protein-coupled receptor (GPCR) activate intracellular signalling partners to varying extents, but the molecular mechanisms that drive these differences remain elusive. ...Distinct ligands for the same G-protein-coupled receptor (GPCR) activate intracellular signalling partners to varying extents, but the molecular mechanisms that drive these differences remain elusive. Here, hypothesizing that such differences in signalling efficacy might be captured structurally in intermediate states under non-equilibrium conditions, we use a time-resolved cryo-electron-microscopy approach to visualize the GTP-induced activation of the Gαβγ heterotrimer by the μ-opioid receptor bound to three ligands that show partial, full or super agonism on the receptor. We resolve ensembles of conformational states along the G-protein activation pathway, including an intermediate state that enables us to visualize receptor dynamics as a function of bound ligand. The results reveal ligand-dependent differences in state occupancy and conformational stability, with higher ligand efficacy correlating with increased dynamics of the receptor's transmembrane helices 5 and 6. Furthermore, we identify key differences between G and G in the mechanism of GTP-induced activation, which are likely to underlie the distinct activation kinetics of these G-protein types. Corroborated by molecular-dynamics simulations and single-molecule fluorescence assays, our findings provide a dynamic structural landscape of GPCR-G-protein interactions for ligands of various efficacies, and suggest that partial agonists produce a 'kinetic trap' during G-protein activation.
History
DepositionApr 27, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70374.png

Downloads & links

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Map

FileDownload / File: emd_70374.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 280 pix.
= 242.956 Å		0.87 Å/pix.
x 280 pix.
= 242.956 Å		0.87 Å/pix.
x 280 pix.
= 242.956 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8677 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.287
Minimum - Maximum-1.1934582 - 1.9299277
Average (Standard dev.)0.00023738382 (±0.04149471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 242.956 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70374_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_70374_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Mu Opioid Receptor Gi1 heterotrimer complex

EntireName: Mu Opioid Receptor Gi1 heterotrimer complex
Components
  • Complex: Mu Opioid Receptor Gi1 heterotrimer complex

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Supramolecule #1: Mu Opioid Receptor Gi1 heterotrimer complex

SupramoleculeName: Mu Opioid Receptor Gi1 heterotrimer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4, #1-#3
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 198050
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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