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- EMDB-71131: A2AR-BRIL in complex with ZM241385 -

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Basic information

Entry
Database: EMDB / ID: EMD-71131
TitleA2AR-BRIL in complex with ZM241385
Map data
Sample
  • Complex: A2AR-BRIL + ZM241385
    • Protein or peptide: Adenosine receptor A2a,Soluble cytochrome b562
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism ...regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism / sensory perception / positive regulation of urine volume / synaptic transmission, dopaminergic / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / synaptic transmission, cholinergic / positive regulation of glutamate secretion / intermediate filament / presynaptic active zone / response to caffeine / blood circulation / eating behavior / inhibitory postsynaptic potential / alpha-actinin binding / regulation of calcium ion transport / asymmetric synapse / axolemma / membrane depolarization / phagocytosis / cellular defense response / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / presynaptic modulation of chemical synaptic transmission / astrocyte activation / response to amphetamine / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / positive regulation of apoptotic signaling pathway / regulation of mitochondrial membrane potential / excitatory postsynaptic potential / synaptic transmission, glutamatergic / apoptotic signaling pathway / locomotory behavior / electron transport chain / negative regulation of inflammatory response / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / vasodilation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / negative regulation of neuron apoptotic process / postsynaptic membrane / calmodulin binding / electron transfer activity / periplasmic space / positive regulation of ERK1 and ERK2 cascade / iron ion binding / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / heme binding / apoptotic process / dendrite / lipid binding / regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / enzyme binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsRao P / Rathinaswamy M / Chan M / Paredes AG / Patel C / Wranik BJ / Powell J / Eaton D / Hicks KJ / Mafi A / Hao Q
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Commun Chem / Year: 2025
Title: Systematic metabolite screening identifies functional regulators of the adenosine A2A receptor.
Authors: Prashant Rao / Manoj Rathinaswamy / Michelle Chan / Andrea Guzmán Paredes / Chirag Patel / Bernd J Wranik / Jonathan Powell / Dan Eaton / Jared Rutter / Kevin G Hicks / Amirhossein Mafi / Qi Hao /
Abstract: The adenosine A2A receptor (A2AR) is a Class A G protein-coupled receptor (GPCR) that regulates inflammation, glucose metabolism, and energy homeostasis in metabolically active tissues. While the ...The adenosine A2A receptor (A2AR) is a Class A G protein-coupled receptor (GPCR) that regulates inflammation, glucose metabolism, and energy homeostasis in metabolically active tissues. While the effects of small-molecule ligands and protein interactions with A2AR have been extensively studied, the regulatory influence of endogenous metabolites remains unexplored. To address this gap, we employed the Mass spectrometry Integrated with equilibrium Dialysis for the discovery of Allostery Systematically (MIDAS) platform to screen a library of human metabolites for interactions with A2AR. This approach identified 180 metabolites that interact with A2AR, including allosteric and orthosteric modulators. We characterized the mechanisms of three metabolites previously unreported to interact with A2AR: prostaglandin D2, an allosteric antagonist that fully inhibits receptor signaling, and two orthosteric agonists, S-adenosyl-L-homocysteine and 2'-deoxyadenosine, that fully activate A2AR. Overall, these findings highlight the potential of the MIDAS platform to uncover previously unrecognized metabolite-GPCR interactions for research and therapeutic applications.
History
DepositionJun 10, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71131.png

Downloads & links

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Map

FileDownload / File: emd_71131.map.gz / Format: CCP4 / Size: 64 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.)
0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00781
Minimum - Maximum-0.14468294 - 0.22402185
Average (Standard dev.)0.0001981741 (±0.003098963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 206.848 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_71131_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_71131_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_71131_half_map_2.map
Projections & Slices
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Sample components

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Entire : A2AR-BRIL + ZM241385

EntireName: A2AR-BRIL + ZM241385
Components
  • Complex: A2AR-BRIL + ZM241385
    • Protein or peptide: Adenosine receptor A2a,Soluble cytochrome b562
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol

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Supramolecule #1: A2AR-BRIL + ZM241385

SupramoleculeName: A2AR-BRIL + ZM241385 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Adenosine receptor A2a,Soluble cytochrome b562

MacromoleculeName: Adenosine receptor A2a,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.803668 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDKMP IMGSSVYITV ELAIAVLAIL GNVLVCWAVW LNSNLQNVTN YFVVSLAAAD ILVGVLAIPF AITISTGFCA ACHGCLFIA CFVLVLAQSS IFSLLAIAID RYIAIAIPLR YNGLVTGTRA AGIIAICWVL SFAIGLTPML GWNNCGQPKE G KAHSQGCG ...String:
DYKDDDDKMP IMGSSVYITV ELAIAVLAIL GNVLVCWAVW LNSNLQNVTN YFVVSLAAAD ILVGVLAIPF AITISTGFCA ACHGCLFIA CFVLVLAQSS IFSLLAIAID RYIAIAIPLR YNGLVTGTRA AGIIAICWVL SFAIGLTPML GWNNCGQPKE G KAHSQGCG EGQVACLFED VVPMNYMVYF NFFACVLVPL LLMLGVYLRI FAAARRQLKA DLEDNWETLN DNLKVIEKAD NA AQVKDAL TKMRAAALDA QKATPPKLED KSPDSPEMKD FRHGFDILVG QIDDALKLAN EGKVKEAQAA AEQLKTTRNA YIQ KYLARS TLQKEVHAAK SAAIIAGLFA LCWLPLHIIN CFTFFCPDCS HAPLWLMYLA IVLAHTNSVV NPFIYAYRIR EFRQ TFRKI IRSHVLRQQE PFKAAHHHHH HHHHH

UniProtKB: Adenosine receptor A2a, Soluble cytochrome b562, Adenosine receptor A2a

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Macromolecule #2: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 1 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #3: 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5...

MacromoleculeName: 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol
type: ligand / ID: 3 / Number of copies: 1 / Formula: ZMA
Molecular weightTheoretical: 337.336 Da
Chemical component information

ChemComp-ZMA:
4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7t32

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 489705
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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