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- EMDB-65996: Cryo-EM structure of GPR84-Gi with DL-175 (foucus receptor) -

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Basic information

Entry
Database: EMDB / ID: EMD-65996
TitleCryo-EM structure of GPR84-Gi with DL-175 (foucus receptor)
Map datamap
Sample
  • Complex: GPR84 with DL-175 (receptor focus)
    • Protein or peptide: GPR84
KeywordsGPCR / SIGNALING PROTEIN / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 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_65996.png

Downloads & links

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Map

FileDownload / File: emd_65996.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 256 pix.
= 257.28 Å		1.01 Å/pix.
x 256 pix.
= 257.28 Å		1.01 Å/pix.
x 256 pix.
= 257.28 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.005 Å
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Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.962915 - 3.891503
Average (Standard dev.)-0.00035559273 (±0.029315664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 257.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65996_msk_1.map
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Half map: A

Fileemd_65996_half_map_1.map
AnnotationA
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Half map: B

Fileemd_65996_half_map_2.map
AnnotationB
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Sample components

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Entire : GPR84 with DL-175 (receptor focus)

EntireName: GPR84 with DL-175 (receptor focus)
Components
  • Complex: GPR84 with DL-175 (receptor focus)
    • Protein or peptide: GPR84

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Supramolecule #1: GPR84 with DL-175 (receptor focus)

SupramoleculeName: GPR84 with DL-175 (receptor focus) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GPR84

MacromoleculeName: GPR84 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGFD ILVGQIDDAL KLANEGKVK EAQAAAEQLK TTRNAYIQKY LWNSSDANFS CYHESVLGYR YVAVSWGVVV AVTGTVGNVL ...String:
MKTIIALSYI FCLVFADYKD DDDKADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGFD ILVGQIDDAL KLANEGKVK EAQAAAEQLK TTRNAYIQKY LWNSSDANFS CYHESVLGYR YVAVSWGVVV AVTGTVGNVL TLLALAIQPK LRTRFNLLIA NLTLADLLYC T LLQPFSVD TYLHLHWRTG ATFCRVFGLL LFASNSVSIL TLCLIALGRY LLIAHPKLFP QVFSAKGIVL ALVSTWVVGV ASFAPLWPIY ILVPVVCTCS FD RIRGRPY TTILMGIYFV LGLSSVGIFY CLIHRQVKRA AQALDQYKLR QASIHSNHVA RTDEAMPGRF QELDSRLASG GPSEGISSEP VSAATTQTLE GDS SEVGDQ INSKRAKQMA EKSPPEASAK AQPIKGARRA PDSSSEFGKV TRMCFAVFLC FALSYIPFLL LNILDARVQA PRVVHMLAAN LTWLNGCINP VLYA AMNRQ FRQAYGSILK RGPRSFHRLH ENLYFQGSVF TLEDFVGDWE QTAAYNLDQV LEQGGVSSLL QNLAVSVTPI QRIVRSGENA LKIDIHVIIP YEGLS ADQM AQIEEVFKVV YPVDDHHFKV ILPYGTLVID GVTPNMLNYF GRPYEGIAVF DGKKITVTGT LWNGNKIIDE RLITPDGSML FRVTINS

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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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 63.4 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 159829
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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