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- EMDB-72202: CryoEM structure of beta2-adrenergic receptor dimer mediated by a... -

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Basic information

Entry
Database: EMDB / ID: EMD-72202
TitleCryoEM structure of beta2-adrenergic receptor dimer mediated by a biased allosteric modulator in lipid nanodisc
Map data
Sample
  • Complex: Dimeric beta2-adrenergic receptor bound to a biased allosteric modulator in nanodisc
    • Protein or peptide: Beta-2 adrenergic receptor
  • Ligand: TETRADECANE
  • Ligand: EICOSANE
  • Ligand: 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one
  • Ligand: 6-bromo-N~4~-cyclohexyl-N~2~-(3,4-difluorophenyl)quinazoline-2,4-diamine
KeywordsGPCR / Adrenergic receptor / Dimer / Molecular glue / Biased allosteric modulator / SIGNALING PROTEIN
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 / potassium channel regulator activity / adenylate cyclase binding / 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 / cell surface receptor signaling pathway / lysosome / signaling receptor complex / 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
Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsShen J / Kobilka BK
Funding support United States, 3 items
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: Nature / Year: 2026
Title: A biased allosteric modulator is a molecular glue for βAR dimerization.
Authors: Jiemin Shen / Teja Nikhil Peddada / Konstantin E Komolov / Francesco De Pascali / Alexander M Garces / Haoqing Wang / Muhammad Ehsan / Pil Seok Chae / Michael T Lerch / Jeffrey L Benovic / ...Authors: Jiemin Shen / Teja Nikhil Peddada / Konstantin E Komolov / Francesco De Pascali / Alexander M Garces / Haoqing Wang / Muhammad Ehsan / Pil Seok Chae / Michael T Lerch / Jeffrey L Benovic / Jun Xu / Brian K Kobilka /
Abstract: Family A G-protein-coupled receptors (GPCRs) are typically described as monomers, yet growing evidence suggests that they can form dimers with distinct signalling properties. However, the mechanisms ...Family A G-protein-coupled receptors (GPCRs) are typically described as monomers, yet growing evidence suggests that they can form dimers with distinct signalling properties. However, the mechanisms and therapeutic potential of such dimerization remain poorly understood. Here we show that AP-7-168, an optimized derivative of a β-arrestin-biased negative allosteric modulator of the β-adrenergic receptor (βAR) that sustains bronchorelaxation in cell and tissue models, functions as a molecular glue to stabilize βAR homodimerization. Cryogenic electron microscopy structures reveal a unique binding mode in which two AP-7-168 molecules pack within a pocket formed by transmembrane helices 3, 4 and 5 of two protomers, stabilizing a dimeric conformation that selectively prevents β-arrestin coupling. In cells, AP-7-168 robustly stabilizes βAR dimerization and drives enlarged nanocluster formation. Combined with extensive functional studies, our findings identify an allosteric mechanism by which a small molecule biases βAR signalling through dimerization, highlighting ligand-stabilized dimerization as a strategy for GPCR modulation.
History
DepositionAug 18, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72202.png

Downloads & links

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Map

FileDownload / File: emd_72202.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.9022914 - 1.1590613
Average (Standard dev.)-0.00018610976 (±0.022030026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72202_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72202_half_map_2.map
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Sample components

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Entire : Dimeric beta2-adrenergic receptor bound to a biased allosteric mo...

EntireName: Dimeric beta2-adrenergic receptor bound to a biased allosteric modulator in nanodisc
Components
  • Complex: Dimeric beta2-adrenergic receptor bound to a biased allosteric modulator in nanodisc
    • Protein or peptide: Beta-2 adrenergic receptor
  • Ligand: TETRADECANE
  • Ligand: EICOSANE
  • Ligand: 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one
  • Ligand: 6-bromo-N~4~-cyclohexyl-N~2~-(3,4-difluorophenyl)quinazoline-2,4-diamine

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Supramolecule #1: Dimeric beta2-adrenergic receptor bound to a biased allosteric mo...

SupramoleculeName: Dimeric beta2-adrenergic receptor bound to a biased allosteric modulator in nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Beta-2 adrenergic receptor

MacromoleculeName: Beta-2 adrenergic receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.767242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAMGQPGN GSAFLLAPNR SHAPDHDVEN LYFQGTQQRD EVWVVGMGIV MSLIVLAIVF GNVLVITAI AKFERLQTVT NYFITSLACA DLVMGLAVVP FGAAHILTKT WTFGNFWCEF WTSIDVLCVT ASIETLCVIA V DRYFAITS ...String:
MKTIIALSYI FCLVFADYKD DDDAMGQPGN GSAFLLAPNR SHAPDHDVEN LYFQGTQQRD EVWVVGMGIV MSLIVLAIVF GNVLVITAI AKFERLQTVT NYFITSLACA DLVMGLAVVP FGAAHILTKT WTFGNFWCEF WTSIDVLCVT ASIETLCVIA V DRYFAITS PFKYQSLLTK NKARVIILMV WIVSGLTSFL PIQMHWYRAT HQEAINCYAE ETCCDFFTNQ AYAIASSIVS FY VPLVIMV FVYSRVFQEA KRQLQKIDKS EGRFHVQNLS QVEQDGRTGH GLRRSSKFCL KEHKALKTLG IIMGTFTLCW LPF FIVNIV HVIQDNLIRK EVYILLNWIG YVNSGFNPLI YCRSPDFRIA FQELLCLRRS SLKAYGNGYS SNGNTGEQSG LEVL FQGPY HVEQEKENKL LAEDLPGTED FVGHQGTVPS DNIDSQGRNA STNDSLLETS QVAPA

UniProtKB: Beta-2 adrenergic receptor

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Macromolecule #2: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 2 / Number of copies: 2 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #3: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 3 / Number of copies: 2 / Formula: LFA
Molecular weightTheoretical: 282.547 Da
Chemical component information

ChemComp-LFA:
EICOSANE

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Macromolecule #4: 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxy...

MacromoleculeName: 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one
type: ligand / ID: 4 / Number of copies: 2 / Formula: P0G
Molecular weightTheoretical: 370.442 Da
Chemical component information

ChemComp-P0G:
8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one

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Macromolecule #5: 6-bromo-N~4~-cyclohexyl-N~2~-(3,4-difluorophenyl)quinazoline-2,4-...

MacromoleculeName: 6-bromo-N~4~-cyclohexyl-N~2~-(3,4-difluorophenyl)quinazoline-2,4-diamine
type: ligand / ID: 5 / Number of copies: 2 / Formula: A1CNS
Molecular weightTheoretical: 433.292 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.0 µm / Nominal defocus min: 0.8 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:

2rh1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 237408
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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