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- PDB-9ehs: Structure of a human adenosine A3 receptor complex bound to the c... -

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Basic information

Entry
Database: PDB / ID: 9ehs
TitleStructure of a human adenosine A3 receptor complex bound to the covalent antagonist LUF7602
Components
  • Adenosine receptor A3,adenosine A3 receptor fused to BRIL
  • BAG2 Anti-BRIL Fab Heavy Chain
  • BAG2 Anti-BRIL Fab Light Chain
  • elbow nanobody
KeywordsSIGNALING PROTEIN / G protein-coupled receptor / adenosine binding / seven transmembrane protein / MEMBRANE 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 / synapse / dendrite / 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 speciessynthetic construct (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang, L. / Mobbs, J.I. / Glukhova, A. / Thal, D.M.
Funding support Australia, 3items
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
CitationJournal: Biorxiv / Year: 2025
Title: Molecular basis of ligand binding and receptor activation at the human A3 adenosine receptor
Authors: Zhang, L. / Mobbs, J.I. / Bennetts, F.M. / Venugopal, H. / Nguyen, A.T. / Christopoulos, A. / van der Es, D. / Heitman, L.H. / May, L.T. / Glukhova, A. / Thal, D.M.
History
DepositionNov 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: BAG2 Anti-BRIL Fab Heavy Chain
K: elbow nanobody
L: BAG2 Anti-BRIL Fab Light Chain
R: Adenosine receptor A3,adenosine A3 receptor fused to BRIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7465
Polymers116,2284
Non-polymers5181
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody BAG2 Anti-BRIL Fab Heavy Chain


Mass: 24539.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Antibody elbow nanobody


Mass: 15071.431 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Antibody BAG2 Anti-BRIL Fab Light Chain


Mass: 23499.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#4: Protein Adenosine receptor A3,adenosine A3 receptor fused to BRIL


Mass: 53118.230 Da / Num. of mol.: 1 / Mutation: S97R mutation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DMS8
#5: Chemical ChemComp-A1BII / LUF7602


Mass: 517.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24FN5O6S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human A3AR-S97R-BRIL-Bag2-Nb complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5127 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 328104 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.81 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00397367
ELECTRON MICROSCOPYf_angle_d0.769210014
ELECTRON MICROSCOPYf_chiral_restr0.0521146
ELECTRON MICROSCOPYf_plane_restr0.00941244
ELECTRON MICROSCOPYf_dihedral_angle_d12.19372625

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