7X5H | pdb_00007x5h

Serotonin 5A (5-HT5A) receptor-Gi protein complex

• PDB DOI: https://doi.org/10.2210/pdb7X5H/pdb
• EM Map EMD-33014: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus, Escherichia coli
• Expression System: Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2022-03-04 Released: 2022-09-14 
• Deposition Author(s): Tan, Y., Xu, P., Huang, S., Xu, H.E., Jiang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into the ligand binding and G i coupling of serotonin receptor 5-HT 5A .

Tan, Y., Xu, P., Huang, S., Yang, G., Zhou, F., He, X., Ma, H., Xu, H.E., Jiang, Y.

(2022) Cell Discov 8: 50-50

• PubMed: 35610220 
• DOI: https://doi.org/10.1038/s41421-022-00412-3
• Primary Citation Related Structures: 
  7X5H


• PubMed Abstract: 
  

  5-hydroxytryptamine receptor 5A (5-HT _5A ) belongs to the 5-HT receptor family and signals through the G _i/o protein. It is involved in nervous system regulation and an attractive target for the treatment of psychosis, depression, schizophrenia, and neuropathic pain. 5-HT _5A is the only G _i/o -coupled 5-HT receptor subtype lacking a high-resolution structure, which hampers the mechanistic understanding of ligand binding and G _i/o coupling for 5-HT _5A . Here we report a cryo-electron microscopy structure of the 5-HT _5A -G _i complex bound to 5-Carboxamidotryptamine (5-CT). Combined with functional analysis, this structure reveals the 5-CT recognition mechanism and identifies the receptor residue at 6.55 as a determinant of the 5-CT selectivity for G _i/o -coupled 5-HT receptors. In addition, 5-HT _5A shows an overall conserved G _i protein coupling mode compared with other G _i/o -coupled 5-HT receptors. These findings provide comprehensive insights into the ligand binding and G protein coupling of G _i/o -coupled 5-HT receptors and offer a template for the design of 5-HT _5A -selective drugs.

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Organizational Affiliation: 
• The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China.
State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Lingang Laboratory, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 196.25 kDa 
• Atom Count: 8,768 
• Modeled Residue Count: 1,128 
• Deposited Residue Count: 1,771 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	371	Homo sapiens	Mutation(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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	70	Homo sapiens	Mutation(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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	D [auth E]	286	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,5-hydroxytryptamine receptor 5A,hydroxytryptamine receptor 5A	E [auth R]	690	Escherichia coli, Homo sapiens	Mutation(s): 0  Gene Names: cybC, HTR5A Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P47898 (Homo sapiens) Explore P47898  Go to UniProtKB:  P47898
PHAROS:  P47898 GTEx:  ENSG00000157219
UniProt Groups	P0ABE7P47898

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8K3 (Subject of Investigation/LOI)	F [auth R]	3-(2-azanylethyl)-1H-indole-5-carboxamide C11 H13 N3 O WKZLNEWVIAGNAW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8K3	BindingDB:  7X5H	Ki: min: 12.58, max: 20 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Tan, Y., Xu, P., Huang, S., Xu, H.E., Jiang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171187

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2022-09-21
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary