9ASA | pdb_00009asa

Global reconstruction of 5-HT2AR bound to RS130-180 in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM)

• PDB DOI: https://doi.org/10.2210/pdb9ASA/pdb
• EM Map EMD-43810: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-02-24 Released: 2025-04-02 
• Deposition Author(s): Gumpper, R.H., Fay, J.F., Roth, B.L.
• Funding Organization(s): Defense Advanced Research Projects Agency (DARPA)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The structural diversity of psychedelic drug actions revealed.

Gumpper, R.H., Jain, M.K., Kim, K., Sun, R., Sun, N., Xu, Z., DiBerto, J.F., Krumm, B.E., Kapolka, N.J., Kaniskan, H.U., Nichols, D.E., Jin, J., Fay, J.F., Roth, B.L.

(2025) Nat Commun 16: 2734-2734

• PubMed: 40108183 
• DOI: https://doi.org/10.1038/s41467-025-57956-7
• Primary Citation of Related Structures:  
  9ARX, 9ARY, 9ARZ, 9AS0, 9AS1, 9AS2, 9AS3, 9AS4, 9AS5, 9AS6, 9AS7, 9AS8, 9AS9, 9ASA


• PubMed Abstract: 
  

  There is currently a resurgence in exploring the utility of classical psychedelics to treat depression, addiction, anxiety disorders, cluster headaches, and many other neuropsychiatric disorders. A biological target of these compounds, and a hypothesized target for their therapeutic actions, is the 5-HT _2A serotonin receptor. Here, we present 7 cryo-EM structures covering all major compound classes of psychedelic and non-psychedelic agonists, including a β-arrestin-biased compound RS130-180. Identifying the molecular interactions between various psychedelics and the 5-HT _2A receptor reveals both common and distinct motifs among the examined psychedelic chemotypes. These findings lead to a broader mechanistic understanding of 5-HT _2A activation, which can catalyze the development of novel chemotypes with potential therapeutic utility and fewer side effects.

---

Organizational Affiliation: 
• Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA. [e-mail].
Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA. [e-mail].
Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon, Korea.
Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
EvE Bio, LLC, Durham, NC, USA.
Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, Baltimore, MD, USA.
Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA. [e-mail].
Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 157.05 kDa 
• Atom Count: 8,163 
• Modeled Residue Count: 1,103 
• Deposited Residue Count: 1,413 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 2A	A	471	Homo sapiens	Mutation(s): 0  Gene Names: HTR2A, HTR2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P28223 (Homo sapiens) Explore P28223  Go to UniProtKB:  P28223
PHAROS:  P28223 GTEx:  ENSG00000102468

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G subunit q (Gi2-mini-Gq chimeric)	B	246	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	358	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
single chain Fab (svFv16)	E	267	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AFX (Subject of Investigation/LOI)	F [auth A]	2,5-dimethoxy-N,N-dimethyl-4-{2-[({2-[(prop-2-yn-1-yl)oxy]phenyl}methyl)amino]ethyl}aniline C22 H28 N2 O3 NDHJMNFRHQYXKX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.12 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: 2025-04-02 
Deposition Author(s): Gumpper, R.H., Fay, J.F., Roth, B.L.

---

Funding Organization	Location	Grant Number
Defense Advanced Research Projects Agency (DARPA)	United States	HR0011-20-2-0029

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Data collection