8JLZ | pdb_00008jlz

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

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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