8JLZ

ST1936-5HT6R complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insight into the selective agonist ST1936 binding of serotonin receptor 5-HT6.

Pei, Y.Wen, X.Guo, S.C.Yang, Z.S.Zhang, R.Xiao, P.Sun, J.P.

(2023) Biochem Biophys Res Commun 671: 327-334

  • DOI: https://doi.org/10.1016/j.bbrc.2023.05.126
  • Primary Citation of Related Structures:  
    8JLZ

  • PubMed Abstract: 

    The serotonin receptor 5-HT 6 R is an important G-protein-coupled receptor (GPCR) that involved in essential functions within the central and peripheral nervous systems and is linked to various psychiatric disorders. Selective activation of 5-HT 6 R promotes neural stem cell regeneration activity. As a 5-HT 6 R selective agonist, 2-(5 chloro-2-methyl-1H-indol-3-yl)-N, N-dimethylethanolamine (ST1936) has been widely used to investigate the functions of the 5-HT 6 R. The molecular mechanism of how ST1936 is recognized by 5-HT 6 R and how it effectively couples with Gs remain unclear. Here, we reconstituted the ST1936-5-HT 6 R-Gs complex in vitro and solved its cryo-electron microscopy structure at 3.1 Å resolution. Further structural analysis and mutational studies facilitated us to identify the residues of the Y310 7.43 and "toggle switch" W281 6.48 of the 5-HT 6 R contributed to the higher efficacy of ST1936 compared with 5-HT. By uncovering the structural foundation of how 5-HT 6 R specifically recognizes agonists and elucidating the molecular process of G protein activation, our discoveries offer valuable insights and pave the way for the development of promising 5-HT 6 R agonists.


  • Organizational Affiliation

    State Key Laboratory of Surface Physics, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education) and Collaborative Innovation Center of Advanced Microstructures, Fudan University, Shanghai, 200433, China; Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short394Homo sapiensMutation(s): 8 
Gene Names: GNASGNAS1GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
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Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]58Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nb35D [auth N]128Camelus bactrianusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 6E [auth R]440Homo sapiensMutation(s): 0 
Gene Names: HTR6
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P50406 (Homo sapiens)
Explore P50406 
Go to UniProtKB:  P50406
PHAROS:  P50406
GTEx:  ENSG00000158748 
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UniProt GroupP50406
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UQL (Subject of Investigation/LOI)
Query on UQL

Download Ideal Coordinates CCD File 
F [auth R]2-(5-chloranyl-2-methyl-1~{H}-indol-3-yl)-N,N-dimethyl-ethanamine
C13 H17 Cl N2
KSYMELKKLOFABL-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UQL BindingDB:  8JLZ Ki: 29 (nM) from 1 assay(s)
IC50: 40 (nM) from 1 assay(s)
EC50: 45 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Structure summary