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- EMDB-61666: A3R-Gi complex bound to NECA (receptor focused) -

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Basic information

Entry
Database: EMDB / ID: EMD-61666
TitleA3R-Gi complex bound to NECA (receptor focused)
Map data
Sample
  • Complex: A3R-Gi complex bound to NECA
KeywordsGPCR / complex / adenosine receptor / adenosine / g protein / SIGNALING PROTEIN
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsOshima HS / Shihoya W / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
CitationJournal: Nat Commun / Year: 2024
Title: Structural insights into the agonist selectivity of the adenosine A receptor.
Authors: Hidetaka S Oshima / Akiko Ogawa / Fumiya K Sano / Hiroaki Akasaka / Tomoyoshi Kawakami / Aika Iwama / Hiroyuki H Okamoto / Chisae Nagiri / Fan-Yan Wei / Wataru Shihoya / Osamu Nureki /
Abstract: Adenosine receptors play pivotal roles in physiological processes. Adenosine A receptor (AR), the most recently identified adenosine receptor, is expressed in various tissues, exhibiting important ...Adenosine receptors play pivotal roles in physiological processes. Adenosine A receptor (AR), 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 AR-selective agents. Recently, we identified RNA-derived N-methyladenosine (mA) as an endogenous agonist for AR, suggesting the relationship between RNA-derived modified adenosine and AR. Despite extensive studies on the other adenosine receptors, the selectivity mechanism of AR, especially for AR-selective agonists such as mA and namodenoson, remained elusive. Here, we identify tRNA-derived N-isopentenyl adenosine (iA) as an AR-selective ligand via screening of modified nucleosides against the adenosine receptors. Like mA, iA is found in the human body and may be an endogenous AR ligand. Our cryo-EM analyses elucidate the AR-G complexes bound to adenosine, 5'-N-ethylcarboxamidoadenosine (NECA), mA, iA, and namodenoson at overall resolutions of 3.27 Å (adenosine), 2.86 Å (NECA), 3.19 Å (mA), 3.28 Å (iA), and 3.20 Å (namodenoson), suggesting the selectivity and activation mechanism of AR. We further conduct structure-guided engineering of mA-insensitive AR, which may aid future research targeting mA and AR, providing a molecular basis for future drug discovery.
History
DepositionSep 24, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61666.png

Downloads & links

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Map

FileDownload / File: emd_61666.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 180 pix.
= 232.2 Å		1.29 Å/pix.
x 180 pix.
= 232.2 Å		1.29 Å/pix.
x 180 pix.
= 232.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.605
Minimum - Maximum-1.3722926 - 2.6404905
Average (Standard dev.)-0.00079103204 (±0.071531504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 232.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61666_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #2

Fileemd_61666_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : A3R-Gi complex bound to NECA

EntireName: A3R-Gi complex bound to NECA
Components
  • Complex: A3R-Gi complex bound to NECA

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Supramolecule #1: A3R-Gi complex bound to NECA

SupramoleculeName: A3R-Gi complex bound to NECA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Ovis aries (sheep)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 210192
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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