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- EMDB-65995: Cryo-EM structure of GPR84 with GLPG1205 -

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Basic information

Entry
Database: EMDB / ID: EMD-65995
TitleCryo-EM structure of GPR84 with GLPG1205
Map datamap
Sample
  • Complex: GPR84 with antagonist
    • Protein or peptide: G-protein coupled receptor 84,Soluble cytochrome b562
  • Ligand: 9-(2-cyclopropylethynyl)-2-[[(2~{S})-1,4-dioxan-2-yl]methoxy]-6,7-dihydropyrimido[6,1-a]isoquinolin-4-one
KeywordsGPCR / SIGNALING PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


urotensin II receptor activity / tertiary granule membrane / specific granule membrane / electron transport chain / neuropeptide signaling pathway / G alpha (s) signalling events / electron transfer activity / periplasmic space / signaling receptor complex / iron ion binding ...urotensin II receptor activity / tertiary granule membrane / specific granule membrane / electron transport chain / neuropeptide signaling pathway / G alpha (s) signalling events / electron transfer activity / periplasmic space / signaling receptor complex / iron ion binding / heme binding / Neutrophil degranulation / plasma membrane
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Soluble cytochrome b562 / G protein-coupled receptor 84
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsSuzuki S / Nishikawa K / Tran DP / Akio K / Fujiyoshi Y
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP24K18061 Japan
Japan Society for the Promotion of Science (JSPS)20H00451 Japan
CitationJournal: Nat Commun / Year: 2026
Title: Mechanistic insight into signal bias by the agonist-dependent conformational dynamics of GPR84.
Authors: Shota Suzuki / Duy Phuoc Tran / Kouki Nishikawa / Akio Kitao / Yoshinori Fujiyoshi /
Abstract: GPR84 is an orphan class A GPCR primarily expressed in immune cells, where it plays key roles in inflammation and metabolism. Here, we present the cryo-electron microscopy structures of the GPR84-Gi ...GPR84 is an orphan class A GPCR primarily expressed in immune cells, where it plays key roles in inflammation and metabolism. Here, we present the cryo-electron microscopy structures of the GPR84-Gi complex bound to the G protein-biased agonist DL-175, and the inactive state of GPR84 bound to the antagonist GLPG1205. Combined with signaling assays and molecular dynamics simulations, these structures elucidate the conformational landscape spanning the inactive and G protein-biased active states of GPR84, providing a mechanistic basis for biased agonism. Notably, steric interactions between DL-175 and L336 selectively preclude the conformational changes required for efficient β-arrestin recruitment without compromising G protein activation. These structural insights provide a structural context for the rational design of GPR84-targeted therapeutics with precisely tuned signaling profiles.
History
DepositionAug 28, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65995.png

Downloads & links

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Map

FileDownload / File: emd_65995.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 320 pix.
= 280.96 Å		0.88 Å/pix.
x 320 pix.
= 280.96 Å		0.88 Å/pix.
x 320 pix.
= 280.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.1881715 - 2.1126504
Average (Standard dev.)-0.00006507909 (±0.022617558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 280.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65995_msk_1.map
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Half map: half A

Fileemd_65995_half_map_1.map
Annotationhalf A
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Half map: half B

Fileemd_65995_half_map_2.map
Annotationhalf B
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Sample components

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Entire : GPR84 with antagonist

EntireName: GPR84 with antagonist
Components
  • Complex: GPR84 with antagonist
    • Protein or peptide: G-protein coupled receptor 84,Soluble cytochrome b562
  • Ligand: 9-(2-cyclopropylethynyl)-2-[[(2~{S})-1,4-dioxan-2-yl]methoxy]-6,7-dihydropyrimido[6,1-a]isoquinolin-4-one

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Supramolecule #1: GPR84 with antagonist

SupramoleculeName: GPR84 with antagonist / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: G-protein coupled receptor 84,Soluble cytochrome b562

MacromoleculeName: G-protein coupled receptor 84,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1
Details: A221-P308 of GPR84 is replaced to thermostabilize the bRIL protein.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.237566 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKWNSSDA NFSCYHESVL GYRYVAVSWG VVVAVTGTVG NVLTLLALAI QPKLRTRFNL LIANLTLAD LLYCTLLQPF SVDTYLHLHW RTGATFCRVF GLLLFASNSV SILTLCLIAL GRYLLIAHPK LFPQVFSAKG I VLALVSTW ...String:
MKTIIALSYI FCLVFADYKD DDDKWNSSDA NFSCYHESVL GYRYVAVSWG VVVAVTGTVG NVLTLLALAI QPKLRTRFNL LIANLTLAD LLYCTLLQPF SVDTYLHLHW RTGATFCRVF GLLLFASNSV SILTLCLIAL GRYLLIAHPK LFPQVFSAKG I VLALVSTW VVGVASFAPL WPIYILVPVV CTCSFDRIRG RPYTTILMGI YFVLGLSSVG IFYCLIHRQV KRAAQALDQY KL RQADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHGF DILVGQIDDA LKL ANEGKV KEAQAAAEQL KTTRNAYIQK YLERARSTLQ KEVDSSSEFG KVTRMCFAVF LCFALSYIPF LLLNILDARV QAPR VVHML AANLTWLNGC INPVLYAAMN RQFRQAYGSI LKRGPRSFHR LH

UniProtKB: G protein-coupled receptor 84, Soluble cytochrome b562, G protein-coupled receptor 84

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Macromolecule #2: 9-(2-cyclopropylethynyl)-2-[[(2~{S})-1,4-dioxan-2-yl]methoxy]-6,7...

MacromoleculeName: 9-(2-cyclopropylethynyl)-2-[[(2~{S})-1,4-dioxan-2-yl]methoxy]-6,7-dihydropyrimido[6,1-a]isoquinolin-4-one
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1L93
Molecular weightTheoretical: 378.421 Da

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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

Concentration10 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 220809
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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