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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
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: To Be Published
Title: Mechanistic insight into signal bias by the agonist-dependent conformational dynamics of GPR84
Authors: Suzuki S / Nishikawa K / Tran DP / Akio K / Fujiyoshi Y
History
DepositionAug 28, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65995.png

Downloads & links

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Map

FileReleased
Annotationmap
Voxel sizeX=Y=Z: 0.878 Å
Density
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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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