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- PDB-9q3l: CryoEM structure of beta2-adrenergic receptor dimer mediated by a... -

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Basic information

Entry
Database: PDB / ID: 9q3l
TitleCryoEM structure of beta2-adrenergic receptor dimer mediated by a biased allosteric modulator in lipid nanodisc
ComponentsBeta-2 adrenergic receptor
KeywordsSIGNALING PROTEIN / GPCR / Adrenergic receptor / Dimer / Molecular glue / Biased allosteric modulator
Function / homology
Function and homology information


beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / AMPA selective glutamate receptor signaling pathway / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / norepinephrine binding / Adrenoceptors / positive regulation of lipophagy / positive regulation of cardiac muscle cell contraction ...beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / AMPA selective glutamate receptor signaling pathway / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / norepinephrine binding / Adrenoceptors / positive regulation of lipophagy / positive regulation of cardiac muscle cell contraction / negative regulation of G protein-coupled receptor signaling pathway / regulation of smooth muscle contraction / adrenergic receptor signaling pathway / response to psychosocial stress / endosome to lysosome transport / positive regulation of glutamate receptor signaling pathway / negative regulation of cardiac muscle cell apoptotic process / adenylate cyclase binding / potassium channel regulator activity / positive regulation of cardiac muscle cell apoptotic process / neuronal dense core vesicle / adenylate cyclase-activating adrenergic receptor signaling pathway / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / cellular response to amyloid-beta / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / Clathrin-mediated endocytosis / G alpha (s) signalling events / positive regulation of MAPK cascade / signaling receptor complex / cell surface receptor signaling pathway / lysosome / endosome / apical plasma membrane / endosome membrane / Ub-specific processing proteases / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / TETRADECANE / EICOSANE / Chem-P0G / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsShen, J. / Kobilka, B.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35 NS137408 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM083118 United States
American Heart Association25POST1411512 United States
CitationJournal: To Be Published
Title: A biased allosteric modulator is a molecular glue for Beta2AR dimerization
Authors: Shen, J. / Peddada, T.N. / Jun, X. / Kobilka, B.K.
History
DepositionAug 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor
B: Beta-2 adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,10410
Polymers103,5342
Non-polymers2,5698
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: Protein Beta-2 adrenergic receptor / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


Mass: 51767.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550
#2: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30
#3: Chemical ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-P0G / 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one


Mass: 370.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26N2O4
#5: Chemical ChemComp-A1CNS / 6-bromo-N~4~-cyclohexyl-N~2~-(3,4-difluorophenyl)quinazoline-2,4-diamine


Mass: 433.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19BrF2N4
Has ligand of interestN
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: Dimeric beta2-adrenergic receptor bound to a biased allosteric modulator in nanodisc
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237408 / Symmetry type: POINT

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