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- EMDB-48065: Structure of a human adenosine A3 receptor complex bound to the c... -

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Basic information

Entry
Database: EMDB / ID: EMD-48065
TitleStructure of a human adenosine A3 receptor complex bound to the covalent antagonist LUF7602
Map dataComposite map
Sample
  • Complex: Human A3AR-S97R-BRIL-Bag2-Nb complex
    • Protein or peptide: BAG2 Anti-BRIL Fab Heavy Chain
    • Protein or peptide: elbow nanobody
    • Protein or peptide: BAG2 Anti-BRIL Fab Light Chain
    • Protein or peptide: Adenosine receptor A3,adenosine A3 receptor fused to BRIL
  • Ligand: LUF7602
KeywordsG protein-coupled receptor / adenosine binding / seven transmembrane protein / MEMBRANE PROTEIN / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of norepinephrine secretion / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / regulation of heart contraction / activation of adenylate cyclase activity / presynaptic modulation of chemical synaptic transmission / negative regulation of cell migration / response to wounding ...regulation of norepinephrine secretion / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / regulation of heart contraction / activation of adenylate cyclase activity / presynaptic modulation of chemical synaptic transmission / negative regulation of cell migration / response to wounding / Schaffer collateral - CA1 synapse / presynaptic membrane / G alpha (i) signalling events / inflammatory response / negative regulation of cell population proliferation / dendrite / synapse / signal transduction / plasma membrane
Similarity search - Function
Adenosine A3 receptor / Adenosine receptor / 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
Adenosine receptor A3
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang L / Mobbs JI / Glukhova A / Thal DM
Funding support Australia, 3 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1196951 Australia
National Health and Medical Research Council (NHMRC, Australia)138448 Australia
Australian Research Council (ARC)LP180100560 Australia
Citation
Journal: Nat Commun / Year: 2025
Title: Molecular basis of ligand binding and receptor activation at the human A adenosine receptor.
Authors: Liudi Zhang / Jesse I Mobbs / Felix M Bennetts / Hariprasad Venugopal / Anh T N Nguyen / Arthur Christopoulos / Daan van der Es / Laura H Heitman / Lauren T May / Alisa Glukhova / David M Thal /
Abstract: Adenosine receptors (ARs: AAR, AAR, AAR, and AAR) are crucial therapeutic targets; however, developing selective, efficacious drugs for them remains a significant challenge. Here, we present high- ...Adenosine receptors (ARs: AAR, AAR, AAR, and AAR) 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 AAR 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 AAR 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-iodobenzyl group of Piclidenoson through a ligand-dependent conformational change of M174. Our comprehensive structural and functional characterisation of AAR 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.
#1: Journal: Biorxiv / Year: 2025
Title: Molecular basis of ligand binding and receptor activation at the human A3 adenosine receptor
Authors: Zhang L / Mobbs JI / Bennetts FM / Venugopal H / Nguyen AT / Christopoulos A / van der Es D / Heitman LH / May LT / Glukhova A / Thal DM
History
DepositionNov 24, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48065.png

Downloads & links

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Map

FileDownload / File: emd_48065.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.65 Å/pix.
x 450 pix.
= 292.5 Å		0.65 Å/pix.
x 450 pix.
= 292.5 Å		0.65 Å/pix.
x 450 pix.
= 292.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 13.0
Minimum - Maximum-1.6470531 - 139.392840000000007
Average (Standard dev.)0.00059615815 (±0.96450394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 292.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human A3AR-S97R-BRIL-Bag2-Nb complex

EntireName: Human A3AR-S97R-BRIL-Bag2-Nb complex
Components
  • Complex: Human A3AR-S97R-BRIL-Bag2-Nb complex
    • Protein or peptide: BAG2 Anti-BRIL Fab Heavy Chain
    • Protein or peptide: elbow nanobody
    • Protein or peptide: BAG2 Anti-BRIL Fab Light Chain
    • Protein or peptide: Adenosine receptor A3,adenosine A3 receptor fused to BRIL
  • Ligand: LUF7602

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Supramolecule #1: Human A3AR-S97R-BRIL-Bag2-Nb complex

SupramoleculeName: Human A3AR-S97R-BRIL-Bag2-Nb complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BAG2 Anti-BRIL Fab Heavy Chain

MacromoleculeName: BAG2 Anti-BRIL Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.539314 KDa
Recombinant expressionOrganism: synthetic construct (others)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCD

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Macromolecule #2: elbow nanobody

MacromoleculeName: elbow nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.071431 KDa
Recombinant expressionOrganism: synthetic construct (others)
SequenceString:
HHHHHHGENL YFQGSQVQLQ ESGGGLVQPG GSLRLSCAAS GRTISRYAMS WFRQAPGKER EFVAVARRSG DGAFYADSVQ GRFTVSRDD AKNTVYLQMN SLKPEDTAVY YCAIDSDTFY SGSYDYWGQG TQVTVSS

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Macromolecule #3: BAG2 Anti-BRIL Fab Light Chain

MacromoleculeName: BAG2 Anti-BRIL Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.499129 KDa
Recombinant expressionOrganism: synthetic construct (others)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: Adenosine receptor A3,adenosine A3 receptor fused to BRIL

MacromoleculeName: Adenosine receptor A3,adenosine A3 receptor fused to BRIL
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.11823 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAMG ANFTPVNGSS GNQSVRLVTS SSLEVLFQGP STALSLANVT YITMEIFIGL CAIVGNVLVI CVVKLNPSLQ TTTFYFIVS LALADIAVGV LVMPLAIVVS LGITIHFYSC LFMTCLLLIF THARIMSLLA IAVDRYLRVK LTVRYKRVTT H RRIWLALG ...String:
DYKDDDDAMG ANFTPVNGSS GNQSVRLVTS SSLEVLFQGP STALSLANVT YITMEIFIGL CAIVGNVLVI CVVKLNPSLQ TTTFYFIVS LALADIAVGV LVMPLAIVVS LGITIHFYSC LFMTCLLLIF THARIMSLLA IAVDRYLRVK LTVRYKRVTT H RRIWLALG LCWLVSFLVG LTPMFGWNMK LTSEYHRAVT FLSCQFVSVM RMDYMVYFSF LTWIFIPLVV MCAIYLDIFY II RNKLADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFRH GFDILVGQID DAL KLANEG KVKEAQAAAE QLKTTRNAYI QKYLERARST LQREFKTAKS LFLVLFLFAL SWLPLSIINC IIYFNGEVPQ LVLY MGILL SHANSMMNPI VYAYKIKKFK ETYLLILKAC VVCHPLEVLF QGPSDSLDTS IEKNSEHHHH HHHH

UniProtKB: Adenosine receptor A3

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Macromolecule #5: LUF7602

MacromoleculeName: LUF7602 / type: ligand / ID: 5 / Number of copies: 1 / Formula: A1BII
Molecular weightTheoretical: 517.53 Da

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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: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 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: INSILICO MODEL / In silico model: Ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 328104
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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