8YH5 | pdb_00008yh5

A3R-Gi complex bound to i6A

PDB DOI: https://doi.org/10.2210/pdb8YH5/pdb
EM Map EMD-39281: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Rattus rattus, Homo sapiens, Bos taurus, Mus musculus, Influenza A virus (A/Victoria/3/1975(H3N2)), Ovis aries, human respiratory syncytial virus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2024-02-27 Released: 2024-11-06
Deposition Author(s): Oshima, H.S., Shihoya, W., Nureki, O.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural insights into the agonist selectivity of the adenosine A 3 receptor.

Oshima, H.S., Ogawa, A., Sano, F.K., Akasaka, H., Kawakami, T., Iwama, A., Okamoto, H.H., Nagiri, C., Wei, F.Y., Shihoya, W., Nureki, O.

(2024) Nat Commun 15: 9294-9294

PubMed: 39511145 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-53473-1
Primary Citation Related Structures:
8YH0, 8YH2, 8YH3, 8YH5, 8YH6

PubMed Abstract:
Adenosine receptors play pivotal roles in physiological processes. Adenosine A ₃ receptor (A ₃R), the most recently identified adenosine receptor, is expressed in various tissues, exhibiting important roles in neuron, heart, and immune cells, and is often overexpressed in tumors, highlighting the therapeutic potential of A ₃R-selective agents. Recently, we identified RNA-derived N ⁶-methyladenosine (m ⁶A) as an endogenous agonist for A ₃R, suggesting the relationship between RNA-derived modified adenosine and A ₃R. Despite extensive studies on the other adenosine receptors, the selectivity mechanism of A ₃R, especially for A ₃R-selective agonists such as m ⁶A and namodenoson, remained elusive. Here, we identify tRNA-derived N ⁶-isopentenyl adenosine (i ⁶A) as an A ₃R-selective ligand via screening of modified nucleosides against the adenosine receptors. Like m ⁶A, i ⁶A is found in the human body and may be an endogenous A ₃R ligand. Our cryo-EM analyses elucidate the A ₃R-G _i complexes bound to adenosine, 5'-N-ethylcarboxamidoadenosine (NECA), m ⁶A, i ⁶A, and namodenoson at overall resolutions of 3.27 Å (adenosine), 2.86 Å (NECA), 3.19 Å (m ⁶A), 3.28 Å (i ⁶A), and 3.20 Å (namodenoson), suggesting the selectivity and activation mechanism of A ₃R. We further conduct structure-guided engineering of m ⁶A-insensitive A ₃R, which may aid future research targeting m ⁶A and A ₃R, providing a molecular basis for future drug discovery.

Organizational Affiliation

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Macromolecule Content

Total Structure Weight: 254.65 kDa
Atom Count: 8,695
Modeled Residue Count: 1,103
Deposited Residue Count: 2,295
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	A [auth B]	375	Rattus rattus	Mutation(s): 0 Gene Names: GNB1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311 Go to UniProtKB: P54311
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54311
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,Guanine nucleotide-binding protein G(i) subunit alpha-1 chimera	B [auth G], D [auth A]	433	Homo sapiens, Bos taurus This entity is chimeric	Mutation(s): 0 Gene Names: GNG2, GNAI1 EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096 Go to UniProtKB: P63096
PHAROS: P63096 GTEx: ENSG00000127955
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
scfv16	C [auth S]	260	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A0B4J1H6 (Mus musculus) Explore A0A0B4J1H6 Go to UniProtKB: A0A0B4J1H6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0B4J1H6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin,Adenosine receptor A3,GFP chimera	E [auth R]	794	Influenza A virus (A/Victoria/3/1975(H3N2)), Ovis aries, human respiratory syncytial virus	Mutation(s): 0 Gene Names: HA, ADORA3 Membrane Entity: Yes
UniProt
Find proteins for P35342 (Ovis aries) Explore P35342 Go to UniProtKB: P35342
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35342
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZIR (Subject of Investigation/LOI) Query on ZIR Download:Ideal Coordinates CCD File SDF format, chain F [auth R] MOL2 format, chain F [auth R] mmCIF format, chain F [auth R]	F [auth R]	N-(3-methylbut-2-en-1-yl)adenosine C₁₅ H₂₁ N₅ O₄ USVMJSALORZVDV-SDBHATRESA-N		Interactions Focus chain F [auth R] Interactions & Density Focus chain F [auth R]