9WIJ | pdb_00009wij

Cryo-EM structure of GPR84 with GLPG1205

PDB DOI: https://doi.org/10.2210/pdb9WIJ/pdb
EM Map EMD-65995: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Escherichia coli
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-08-28 Released: 2026-07-01
Deposition Author(s): Suzuki, S., Nishikawa, K., Tran, D.P., Akio, K., Fujiyoshi, Y.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9WIJ

This is version 1.0 of the entry. See complete history.

Literature

Mechanistic insight into signal bias by the agonist-dependent conformational dynamics of GPR84

Suzuki, S., Nishikawa, K., Tran, D.P., Akio, K., Fujiyoshi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 50.62 kDa
Atom Count: 2,312
Modeled Residue Count: 290
Deposited Residue Count: 447
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor 84,Soluble cytochrome b562	A	447	Homo sapiens, Escherichia coli	Mutation(s): 0 Gene Names: GPR84, EX33, cybC
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQS5 (Homo sapiens) Explore Q9NQS5 Go to UniProtKB: Q9NQS5
PHAROS: Q9NQS5 GTEx: ENSG00000139572
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q9NQS5 P0ABE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L93( Subject of Investigation/LOI) Query on A1L93 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	9-(2-cyclopropylethynyl)-2-[[(2~{S})-1,4-dioxan-2-yl]methoxy]-6,7-dihydropyrimido[6,1-a]isoquinolin-4-one C₂₂ H₂₂ N₂ O₄ IRBAWVGZNJIROV-SFHVURJKSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP24K18061
Japan Society for the Promotion of Science (JSPS)	Japan	20H00451

Revision History (Full details and data files)

Version 1.0: 2026-07-01
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.