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- PDB-9wij: Cryo-EM structure of GPR84 with GLPG1205 -

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Basic information

Entry
Database: PDB / ID: 9wij
TitleCryo-EM structure of GPR84 with GLPG1205
ComponentsG-protein coupled receptor 84,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / GPCR / SIGNALING PROTEIN
Function / homology
Function and homology information


urotensin II receptor activity / tertiary granule membrane / specific granule membrane / neuropeptide signaling pathway / electron transport chain / 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 / neuropeptide signaling pathway / electron transport chain / 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)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsSuzuki, S. / Nishikawa, K. / Tran, D.P. / Akio, K. / Fujiyoshi, Y.
Funding support Japan, 2items
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, D.P. / Akio, K. / Fujiyoshi, Y.
History
DepositionAug 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: G-protein coupled receptor 84,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6162
Polymers50,2381
Non-polymers3781
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein G-protein coupled receptor 84,Soluble cytochrome b562 / Inflammation-related G-protein coupled receptor EX33 / Cytochrome b-562


Mass: 50237.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A221-P308 of GPR84 is replaced to thermostabilize the bRIL protein.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: GPR84, EX33, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NQS5, UniProt: P0ABE7
#2: Chemical ChemComp-A1L93 / 9-(2-cyclopropylethynyl)-2-[[(2~{S})-1,4-dioxan-2-yl]methoxy]-6,7-dihydropyrimido[6,1-a]isoquinolin-4-one


Mass: 378.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N2O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GPR84 with antagonist / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Escherichia coli (E. coli)562
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220809 / Algorithm: BACK PROJECTION / Symmetry type: POINT

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