8FYX | pdb_00008fyx

Buspirone-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8FYX

This is version 1.3 of the entry. See complete history

Literature

Structural pharmacology and therapeutic potential of 5-methoxytryptamines.

Warren, A.L.Lankri, D.Cunningham, M.J.Serrano, I.C.Parise, L.F.Kruegel, A.C.Duggan, P.Zilberg, G.Capper, M.J.Havel, V.Russo, S.J.Sames, D.Wacker, D.

(2024) Nature 630: 237-246

  • DOI: https://doi.org/10.1038/s41586-024-07403-2
  • Primary Citation Related Structures: 
    8FY8, 8FYE, 8FYL, 8FYT, 8FYX

  • PubMed Abstract: 

    Psychedelic substances such as lysergic acid diethylamide (LSD) and psilocybin show potential for the treatment of various neuropsychiatric disorders 1-3 . These compounds are thought to mediate their hallucinogenic and therapeutic effects through the serotonin (5-hydroxytryptamine (5-HT)) receptor 5-HT 2A (ref. 4 ). However, 5-HT 1A also plays a part in the behavioural effects of tryptamine hallucinogens 5 , particularly 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT), a psychedelic found in the toxin of Colorado River toads 6 . Although 5-HT 1A is a validated therapeutic target 7,8 , little is known about how psychedelics engage 5-HT 1A and which effects are mediated by this receptor. Here we map the molecular underpinnings of 5-MeO-DMT pharmacology through five cryogenic electron microscopy (cryo-EM) structures of 5-HT 1A , systematic medicinal chemistry, receptor mutagenesis and mouse behaviour. Structure-activity relationship analyses of 5-methoxytryptamines at both 5-HT 1A and 5-HT 2A enable the characterization of molecular determinants of 5-HT 1A signalling potency, efficacy and selectivity. Moreover, we contrast the structural interactions and in vitro pharmacology of 5-MeO-DMT and analogues to the pan-serotonergic agonist LSD and clinically used 5-HT 1A agonists. We show that a 5-HT 1A -selective 5-MeO-DMT analogue is devoid of hallucinogenic-like effects while retaining anxiolytic-like and antidepressant-like activity in socially defeated animals. Our studies uncover molecular aspects of 5-HT 1A -targeted psychedelics and therapeutics, which may facilitate the future development of new medications for neuropsychiatric disorders.


  • Organizational Affiliation
    • Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 151.93 kDa 
  • Atom Count: 7,325 
  • Modeled Residue Count: 914 
  • Deposited Residue Count: 1,344 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63096
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1358Homo sapiensMutation(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 Groups
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UniProt GroupP62873
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]80Homo sapiensMutation(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 Groups
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UniProt GroupP59768
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,5-hydroxytryptamine receptor 1A,5-hydroxytryptamine receptor 1AD [auth R]552Homo sapiensMutation(s): 1 
Gene Names: cybCHTR1AADRB2RL1ADRBRL1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P08908 (Homo sapiens)
Explore P08908 
Go to UniProtKB:  P08908
PHAROS:  P08908
GTEx:  ENSG00000178394 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P08908
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J40

Query on J40



Download:Ideal Coordinates CCD File
F [auth R][(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5E,8E)-hexadeca-5,8,11,14-tetraenoate
C39 H68 O16 P2
KFDYJTVTHSTWNE-UDQXHECVSA-N
Y01

Query on Y01



Download:Ideal Coordinates CCD File
G [auth R],
H [auth R]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
YLX
(Subject of Investigation/LOI)

Query on YLX



Download:Ideal Coordinates CCD File
E [auth R]Buspirone
C21 H31 N5 O2
QWCRAEMEVRGPNT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
YLX BindingDB:  8FYX Ki: min: 3.1, max: 891.25 (nM) from 48 assay(s)
IC50: min: 7.1, max: 1000 (nM) from 12 assay(s)
EC50: min: 15, max: 186 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
MODEL REFINEMENTREFMAC
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM 133504
Other privateEdward Mallinckrodt, Jr. Foundation
Other privateAlfred P Sloan Foundationuroscience
Other privateMcKnight Foundation
Other privateIrma T. Hirschl/Monique Weill-Caulier Trust

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Database references
  • Version 1.3: 2024-11-06
    Changes: Data collection, Structure summary