7E2X

Apo serotonin 1A (5-HT1A) receptor-Gi protein complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the lipid and ligand regulation of serotonin receptors.

Xu, P.Huang, S.Zhang, H.Mao, C.Zhou, X.E.Cheng, X.Simon, I.A.Shen, D.D.Yen, H.Y.Robinson, C.V.Harpsoe, K.Svensson, B.Guo, J.Jiang, H.Gloriam, D.E.Melcher, K.Jiang, Y.Zhang, Y.Xu, H.E.

(2021) Nature 592: 469-473

  • DOI: https://doi.org/10.1038/s41586-021-03376-8
  • Primary Citation of Related Structures:  
    7E2X, 7E2Y, 7E2Z, 7E32, 7E33

  • PubMed Abstract: 

    Serotonin, or 5-hydroxytryptamine (5-HT), is an important neurotransmitter 1,2 that activates the largest subtype family of G-protein-coupled receptors 3 . Drugs that target 5-HT 1A , 5-HT 1D , 5-HT 1E and other 5-HT receptors are used to treat numerous disorders 4 . 5-HT receptors have high levels of basal activity and are subject to regulation by lipids, but the structural basis for the lipid regulation and basal activation of these receptors and the pan-agonism of 5-HT remains unclear. Here we report five structures of 5-HT receptor-G-protein complexes: 5-HT 1A in the apo state, bound to 5-HT or bound to the antipsychotic drug aripiprazole; 5-HT 1D bound to 5-HT; and 5-HT 1E in complex with a 5-HT 1E - and 5-HT 1F -selective agonist, BRL-54443. Notably, the phospholipid phosphatidylinositol 4-phosphate is present at the G-protein-5-HT 1A interface, and is able to increase 5-HT 1A -mediated G-protein activity. The receptor transmembrane domain is surrounded by cholesterol molecules-particularly in the case of 5-HT 1A , in which cholesterol molecules are directly involved in shaping the ligand-binding pocket that determines the specificity for aripiprazol. Within the ligand-binding pocket of apo-5-HT 1A are structured water molecules that mimic 5-HT to activate the receptor. Together, our results address a long-standing question of how lipids and water molecules regulate G-protein-coupled receptors, reveal how 5-HT acts as a pan-agonist, and identify the determinants of drug recognition in 5-HT receptors.


  • Organizational Affiliation

    Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1345Homo 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
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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]71Homo 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 
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UniProt GroupP59768
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,5-hydroxytryptamine receptor 1AD [auth R]543Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 4 
Gene Names: cybCHTR1AADRB2RL1ADRBRL1
Membrane Entity: Yes 
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Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P08908 (Homo sapiens)
Explore P08908 
Go to UniProtKB:  P08908
PHAROS:  P08908
GTEx:  ENSG00000178394 
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 (Subject of Investigation/LOI)
Query on J40

Download Ideal Coordinates CCD File 
E [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 (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
F [auth R]
G [auth R]
H [auth R]
I [auth R]
K [auth R]
F [auth R],
G [auth R],
H [auth R],
I [auth R],
K [auth R],
L [auth R],
M [auth R],
N [auth R],
O [auth R],
P [auth R]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
J [auth R],
Q [auth R],
R
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770796

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary