9MD1 | pdb_00009md1

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural determinants of G protein subtype selectivity at the serotonin receptor 5-HT1A.

Warren, A.L.Zilberg, G.Abbassi, A.Abraham, A.Yang, S.Wacker, D.

(2025) Sci Adv 11: eadu9851-eadu9851

  • DOI: https://doi.org/10.1126/sciadv.adu9851
  • Primary Citation of Related Structures:  
    9DYD, 9DYE, 9DYF, 9MD1

  • PubMed Abstract: 

    Activation of the serotonin receptor 5-HT1A has been shown to regulate mood and cognition, making 5-HT1A an important target in the treatment of anxiety, depression, and psychosis. Although the receptor signals through inhibitory G proteins, more work is necessary to understand differences in transducer coupling and its relation to functional activity. To develop a molecular understanding of the differences underlying transducer coupling and activation, we performed structure-activity relationship studies of 5-HT1A with distinct G proteins. Through a combination of in vitro assays, we identified a potent partial agonist that selectively engages a G protein subtype. We further investigated the differences in G protein engagement at 5-HT1A with cryo-electron microscopy, determining structures of 5-HT1A bound to distinct ligands and G protein subtypes. Combined with subsequent structure-guided mutagenesis and signaling assays, our studies uncover both orthosteric and allosteric determinants of agonist-specific stimulation of distinct transducers.


  • Organizational Affiliation
    • Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(z) subunit alpha355Homo sapiensMutation(s): 0 
Gene Names: GNAZ
UniProt & NIH Common Fund Data Resources
Find proteins for P19086 (Homo sapiens)
Explore P19086 
Go to UniProtKB:  P19086
PHAROS:  P19086
GTEx:  ENSG00000128266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19086
Sequence Annotations
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  • Reference Sequence
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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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,5-hydroxytryptamine receptor 1AC,
E [auth R]
552Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 1 
Gene Names: cybCHTR1AADRB2RL1ADRBRL1
UniProt & NIH Common Fund Data Resources
Find proteins for P08908 (Homo sapiens)
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Go to UniProtKB:  P08908
PHAROS:  P08908
GTEx:  ENSG00000178394 
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UniProt GroupP08908
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]80Homo sapiensMutation(s): 0 
Gene Names: GNG2
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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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J40
Query on J40

Download Ideal Coordinates CCD File 
K [auth C],
Q [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
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth C]
H [auth C]
I [auth C]
J [auth C]
M [auth R]
G [auth C],
H [auth C],
I [auth C],
J [auth C],
M [auth R],
N [auth R],
O [auth R],
P [auth R]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
YLX (Subject of Investigation/LOI)
Query on YLX

Download Ideal Coordinates CCD File 
F [auth C],
L [auth R]
Buspirone
C21 H31 N5 O2
QWCRAEMEVRGPNT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
MODEL REFINEMENTREFMAC
RECONSTRUCTIONcryoSPARC

Structure Validation

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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 privateMcKnight Foundation
Other privateIrma T. Hirschl/Monique Weill-Caulier Trust

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release