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- EMDB-65999: Cryo-EM structure of GPR84-Gi complex with DL-175 -

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Basic information

Entry
Database: EMDB / ID: EMD-65999
TitleCryo-EM structure of GPR84-Gi complex with DL-175
Map datacompositmap
Sample
  • Complex: GPR84 with antagonist
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Soluble cytochrome b562,G-protein coupled receptor 84,LgBiT tag
    • Protein or peptide: ScFv16
  • Ligand: 3-[2-(4-chloranylnaphthalen-1-yl)oxyethyl]-1-oxidanidyl-pyridin-1-ium
KeywordsGPCR / SIGNALING PROTEIN / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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_65999.png

Downloads & links

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Map

FileDownload / File: emd_65999.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcompositmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.005 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-42.713374999999999 - 57.514923000000003
Average (Standard dev.)-0.007238152 (±1.0596509)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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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: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Soluble cytochrome b562,G-protein coupled receptor 84,LgBiT tag
    • Protein or peptide: ScFv16
  • Ligand: 3-[2-(4-chloranylnaphthalen-1-yl)oxyethyl]-1-oxidanidyl-pyridin-1-ium

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Supramolecule #1: GPR84 with antagonist

SupramoleculeName: GPR84 with antagonist / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.414047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHASM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Details: N-terminus His tag C-terminus Linker and HiBiT tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.772562 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHE NLYFQGSSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSA SQDGKLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT G YLSCCRFL ...String:
MHHHHHHHHE NLYFQGSSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSA SQDGKLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT G YLSCCRFL DDNQIVTSSG DTTCALWDIE TGQQTTTFTG HTGDVMSLSL APDTRLFVSG ACDASAKLWD VREGMCRQTF TG HESDINA ICFFPNGNAF ATGSDDATCR LFDLRADQEL MTYSHDNIIC GITSVSFSKS GRLLLAGYDD FNCNVWDALK ADR AGVLAG HDNRVSCLGV TDDGMAVATG SWDSFLKIWN GGSGGGGSGG SSSGGVSGWR LFKKIS

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.729947 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFCAIL

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: Soluble cytochrome b562,G-protein coupled receptor 84,LgBiT tag

MacromoleculeName: Soluble cytochrome b562,G-protein coupled receptor 84,LgBiT tag
type: protein_or_peptide / ID: 4
Details: N-terminus HAtag, FLAG tag, bRIL C-terminus LgBiT tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 76.73525 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LWNSSDANFS CYHESVLGYR YVAVSWGVVV A VTGTVGNV ...String:
MKTIIALSYI FCLVFADYKD DDDKADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LWNSSDANFS CYHESVLGYR YVAVSWGVVV A VTGTVGNV LTLLALAIQP KLRTRFNLLI ANLTLADLLY CTLLQPFSVD TYLHLHWRTG ATFCRVFGLL LFASNSVSIL TL CLIALGR YLLIAHPKLF PQVFSAKGIV LALVSTWVVG VASFAPLWPI YILVPVVCTC SFDRIRGRPY TTILMGIYFV LGL SSVGIF YCLIHRQVKR AAQALDQYKL RQASIHSNHV ARTDEAMPGR FQELDSRLAS GGPSEGISSE PVSAATTQTL EGDS SEVGD QINSKRAKQM AEKSPPEASA KAQPIKGARR APDSSSEFGK VTRMCFAVFL CFALSYIPFL LLNILDARVQ APRVV HMLA ANLTWLNGCI NPVLYAAMNR QFRQAYGSIL KRGPRSFHRL HENLYFQGSV FTLEDFVGDW EQTAAYNLDQ VLEQGG VSS LLQNLAVSVT PIQRIVRSGE NALKIDIHVI IPYEGLSADQ MAQIEEVFKV VYPVDDHHFK VILPYGTLVI DGVTPNM LN YFGRPYEGIA VFDGKKITVT GTLWNGNKII DERLITPDGS MLFRVTINS

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

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Macromolecule #5: ScFv16

MacromoleculeName: ScFv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 26.466486 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL K

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Macromolecule #6: 3-[2-(4-chloranylnaphthalen-1-yl)oxyethyl]-1-oxidanidyl-pyridin-1-ium

MacromoleculeName: 3-[2-(4-chloranylnaphthalen-1-yl)oxyethyl]-1-oxidanidyl-pyridin-1-ium
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1MBR
Molecular weightTheoretical: 299.752 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 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 159829
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER

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