9EBH | pdb_00009ebh

Human adenosine A3 receptor Gi1 complex bound to adenosine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9EBH

This is version 1.1 of the entry. See complete history

Literature

Molecular basis of ligand binding and receptor activation at the human A 3 adenosine receptor.

Zhang, L.Mobbs, J.I.Bennetts, F.M.Venugopal, H.Nguyen, A.T.N.Christopoulos, A.van der Es, D.Heitman, L.H.May, L.T.Glukhova, A.Thal, D.M.

(2025) Nat Commun 16: 7674-7674

  • DOI: https://doi.org/10.1038/s41467-025-62872-x
  • Primary Citation Related Structures: 
    9EBH, 9EBI, 9EHS

  • PubMed Abstract: 

    Adenosine receptors (ARs: A 1 AR, A 2A AR, A 2B AR, and A 3 AR) are crucial therapeutic targets; however, developing selective, efficacious drugs for them remains a significant challenge. Here, we present high-resolution cryo-electron microscopy (cryo-EM) structures of the human A 3 AR in three distinct functional states: bound to the endogenous agonist adenosine, the clinically relevant agonist Piclidenoson, and the covalent antagonist LUF7602. These structures, complemented by mutagenesis and pharmacological studies, reveal an A 3 AR activation mechanism that involves an extensive hydrogen bond network from the extracellular surface down to the orthosteric binding site. In addition, we identify a cryptic pocket that accommodates the N 6 -iodobenzyl group of Piclidenoson through a ligand-dependent conformational change of M174 5.35 . Our comprehensive structural and functional characterisation of A 3 AR advances our understanding of adenosine receptor pharmacology and establishes a foundation for developing more selective therapeutics for various disorders, including inflammatory diseases, cancer, and glaucoma.


  • Organizational Affiliation
    • Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia.

Macromolecule Content 

  • Total Structure Weight: 154.48 kDa 
  • Atom Count: 8,612 
  • Modeled Residue Count: 1,097 
  • Deposited Residue Count: 1,384 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1349Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody fragment scFv16|Mus musculus (10090)C [auth E]248Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]70Homo sapiensMutation(s): 0 
Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
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Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Adenosine receptor A3E [auth R]363Homo sapiensMutation(s): 0 
Gene Names: ADORA3
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Go to UniProtKB:  P0DMS8
PHAROS:  P0DMS8
GTEx:  ENSG00000282608 
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UniProt GroupP0DMS8
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADN
(Subject of Investigation/LOI)

Query on ADN



Download:Ideal Coordinates CCD File
F [auth R]ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5127

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1196951
National Health and Medical Research Council (NHMRC, Australia)Australia138448
Australian Research Council (ARC)AustraliaLP180100560

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references