9BUY | pdb_00009buy

Structure of the LM189-Bound beta2AR-Gi Complex

• PDB DOI: https://doi.org/10.2210/pdb9BUY/pdb
• EM Map EMD-44925: EMDB EMDataResource

• Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Trichoplusia ni, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-05-17 Released: 2025-05-28 
• Deposition Author(s): Casiraghi, M., Wang, H., Kobilka, B.K.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and dynamics determine G protein coupling specificity at a class A GPCR.

Casiraghi, M., Wang, H., Brennan, P.C., Habrian, C., Hubner, H., Schmidt, M.F., Maul, L., Pani, B., Bahriz, S.M.F.M., Xu, B., Staffen, N., Assafa, T.E., Chen, B., White, E., Sunahara, R.K., Inoue, A., Xiang, Y.K., Lefkowitz, R.J., Isacoff, E.Y., Nucci, N., Gmeiner, P., Lerch, M.T., Kobilka, B.K.

(2025) Sci Adv 11: eadq3971-eadq3971

• PubMed: 40106559 
• DOI: https://doi.org/10.1126/sciadv.adq3971
• Primary Citation of Related Structures:  
  9BUY


• PubMed Abstract: 
  

  G protein-coupled receptors (GPCRs) exhibit varying degrees of selectivity for different G protein isoforms. Despite the abundant structures of GPCR-G protein complexes, little is known about the mechanism of G protein coupling specificity. The β ₂ -adrenergic receptor is an example of GPCR with high selectivity for Gαs, the stimulatory G protein for adenylyl cyclase, and much weaker for the Gαi family of G proteins inhibiting adenylyl cyclase. By developing a Gαi-biased agonist (LM189), we provide structural and biophysical evidence supporting that distinct conformations at ICL2 and TM6 are required for coupling of the different G protein subtypes Gαs and Gαi. These results deepen our understanding of G protein specificity and bias and can accelerate the design of ligands that select for preferred signaling pathways.

---

Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, USA.
Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
FAU NeW, Erlangen, Germany.
Department of Medicine, Duke University Medical Center, Durham, NC, USA.
Department of Pharmacology, University of California, Davis, Davis, CA, USA.
VA Northern California Health Care System, Mather, CA, USA.
Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.
Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.
Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.
Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.
Department of Biochemistry, Duke University Medical Center, Durham, NC, USA.
HHMI, Duke University Medical Center, Durham, NC, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
Department of Physics and Astronomy and Department of Biological and Biomedical Biosciences, Rowan University, Glassboro, NJ, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 167.73 kDa 
• Atom Count: 8,640 
• Modeled Residue Count: 1,117 
• Deposited Residue Count: 1,488 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	344	Homo sapiens	Mutation(s): 0  Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
PHAROS:  P62873 GTEx:  ENSG00000078369

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	D [auth E]	259	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2 adrenergic receptor	E [auth R]	460	Homo sapiens	Mutation(s): 0  Gene Names: ADRB2, ADRB2R, B2AR
UniProt & NIH Common Fund Data Resources
Find proteins for P07550 (Homo sapiens) Explore P07550  Go to UniProtKB:  P07550
PHAROS:  P07550 GTEx:  ENSG00000169252

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KBY	J [auth R]	N-[(3R)-4-(4-tert-butylphenyl)-3-({2-[(4-methoxyphenyl)sulfanyl]-5-[methyl(propan-2-yl)sulfamoyl]benzene-1-carbonyl}amino)butanoyl]glycine C34 H43 N3 O7 S2 POBZRCRFILRWTQ-RUZDIDTESA-N
A1ASM (Subject of Investigation/LOI)	I [auth R]	4-[(1R)-1-hydroxy-2-{[6-(4-phenylbutoxy)hexyl]amino}ethyl]benzene-1,2-diol C24 H35 N O4 PTCUGZHAMATNBH-DEOSSOPVSA-N
CLR	F [auth R], G [auth R], H [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Casiraghi, M., Wang, H., Kobilka, B.K.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS028471

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release