Cryo‐EM structure of G‐protein‐coupled receptor GPR17 in complex with inhibitory G protein

Ye, Fang; Wong, Thian‐Sze; Chen, Geng; Zhang, Zhiyi; Zhang, Binghao; Gan, Shiyi; Gao, Wei; Li, Jiancheng; Wu, Zhangsong; pan, xin; Du, Yang

doi:10.1002/mco2.159

Cited by 20 publications

(20 citation statements)

References 28 publications

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“…The van der Waals (−18.11 kcal/mol for site 1 and −26.281 kcal/mol for site 2) and coulomb interaction energy (−28.35 kcal/mol for site 1 and −31.63 kcal/mol for site 2) between GPR17 receptor and UDP at both ligand binding sites is better comparable from our observations. The result of molecular docking of UDP in two binding sites of GPR17 implies the formation of strong interactions, and further, it is of interest to check whether UDP can bind both sites of the GPR17 receptor simultaneously 26 . We performed docking of GPR17‐UDP in the site 1 complex with UDP at site 2 and vice versa to validate our assumption.…”

Section: Resultsmentioning

confidence: 91%

“…The result of molecular docking of UDP in two binding sites of GPR17 implies the formation of strong interactions, and further, it is of interest to check whether UDP can bind both sites of the GPR17 receptor simultaneously. 26 We performed docking of GPR17-UDP in the site 1 complex with UDP at site 2 and vice versa to validate our assumption. The molecular docking resulted in a poor glide score (−3.83 kcal/mol), implying the non-probable binding of UDP at dual ligand binding sites of the GPR17 receptor.…”

Section: Endogenous and Synthetic Ligands Bind With Dual Sites Of Gpr17mentioning

confidence: 89%

“…Recently, cryo-electron microscopy (cryo-EM) of a long isoform of GPR17 in complex with Gi protein was identified. 26 Since the 3D structure of short isoform, GPR17 is not resolved, 27 and its ligand binding sites have not yet been identified experimentally. Thus the computational approaches have been used effectively to predict the ligand binding sites.…”

Section: Introductionmentioning

confidence: 99%

“…Considering the structural conjunction of P2Y with GPR17, we hypothesize that GPR17 may have dual ligand binding sites. Recently, cryo‐electron microscopy (cryo‐EM) of a long isoform of GPR17 in complex with Gi protein was identified 26 . Since the 3D structure of short isoform, GPR17 is not resolved, 27 and its ligand binding sites have not yet been identified experimentally.…”

Section: Introductionmentioning

confidence: 99%

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Structural analysis of human G‐protein‐coupled receptor 17 ligand binding sites

Mani

Ramesh

Yli‐Harja

et al. 2023

J of Cellular Biochemistry

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The human G protein coupled membrane receptor (GPR17), the sensor of brain damage, is identified as a biomarker for many neurological diseases. In human brain tissue, GPR17 exist in two isoforms, long and short. While cryo‐electron microscopy technology has provided the structure of the long isoform of GPR17 with Gi complex, the structure of the short isoform and its activation mechanism remains unclear. Recently, we theoretically modeled the structure of the short isoform of GPR17 with Gi signaling protein and identified novel ligands. In the present work, we demonstrated the presence of two distinct ligand binding sites in the short isoform of GPR17. The molecular docking of GPR17 with endogenous (UDP) and synthetic ligands (T0510.3657, MDL29950) found the presence of two distinct binding pockets. Our observations revealed that endogenous ligand UDP can bind stronger in two different binding pockets as evidenced by glide and autodock vina scores, whereas the other two ligand's binding with GPR17 has less docking score. The analysis of receptor−UDP interactions shows complexes' stability in the lipid environment by 100 ns atomic molecular dynamics simulations. The amino acid residues VAL83, ARG87, and PHE111 constitute ligand binding site 1, whereas site 2 constitutes ASN67, ARG129, and LYS232. Root mean square fluctuation analysis showed the residues 83, 87, and 232 with higher fluctuations during molecular dynamics simulation in both binding pockets. Our findings imply that the residues of GPR17's two binding sites are crucial, and their interaction with UDP reveals the protein's hidden signaling and communication properties. Furthermore, this finding may assist in the development of targeted therapies for the treatment of neurological diseases.

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Section: Resultsmentioning

confidence: 91%

Section: Endogenous and Synthetic Ligands Bind With Dual Sites Of Gpr17mentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Structural analysis of human G‐protein‐coupled receptor 17 ligand binding sites

Mani

Ramesh

Yli‐Harja

et al. 2023

J of Cellular Biochemistry

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show abstract

“…Many oGPCRs including the adhesion family (aGPCRs) are constitutively active receptors, presenting additional technical hurdles for deorphanization 8 . Since the report of the first ligand-free orphan GPR52 structure by Lin et al 2 , several structures of oGPCRs in complex with G proteins in the absence of exogenous ligand stimulation have been determined—such as GPR17-Gi 9 , GPR88-Gi 10 , GPR119-Gs 11 and aGPCR-G protein complexes 12 – 15 . All these oGPCRs were activated by either their own motif or an endogenous lipid from the cell membrane: the receptor’s extracellular loop 2 (ECL2) folds into the orthosteric pocket and functions as a built-in agonist for GPR52 2 and GPR17; 9 the “stalk” region functions as a tethered agonist for aGPCRs; 12 – 15 an unassigned density in the orthosteric pocket may represent a putative endogenous ligand for GPR88; 10 a lipid molecule occupies the orthosteric pocket responsible for the high basal activity of GPR119 11 .…”

Section: Introductionmentioning

confidence: 99%

The activation mechanism and antibody binding mode for orphan GPR20

Lin

Jiang

et al. 2023

Cell Discov

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GPR20 is a class-A orphan G protein-coupled receptor (GPCR) and a potential therapeutic target for gastrointestinal stromal tumors (GIST) owing to its differentially high expression. An antibody-drug conjugate (ADC) containing a GPR20-binding antibody (Ab046) was recently developed in clinical trials for GIST treatment. GPR20 constitutively activates Gi proteins in the absence of any known ligand, but it remains obscure how this high basal activity is achieved. Here we report three cryo-EM structures of human GPR20 complexes including Gi-coupled GPR20 in the absence or presence of the Fab fragment of Ab046 and Gi-free GPR20. Remarkably, the structures demonstrate a uniquely folded N-terminal helix capping onto the transmembrane domain and our mutagenesis study suggests a key role of this cap region in stimulating the basal activity of GPR20. We also uncover the molecular interactions between GPR20 and Ab046, which may enable the design of tool antibodies with enhanced affinity or new functionality for GPR20. Furthermore, we report the orthosteric pocket occupied by an unassigned density which might be essential for exploring opportunities for deorphanization.

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Cryo‐EM structure of orphan G protein‐coupled receptor GPR21

Wong

Gao

Chen

et al. 2023

MedComm

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GPR21 belongs to class A orphan G protein‐coupled receptor (GPCR). The endogenous ligands for human GPR21 remain unidentified. GPR21 expression is associated with developing type 2 diabetes (T2DM), a multifactorial metabolic disease caused by pancreatic β‐cell dysfunction, decreasing insulin production, insulin resistance, and obesity. Animal studies suggested that GPR21 is a potential therapeutic target for T2DM treatment. The underlying mechanisms leading to GPR21 self‐activation remain unknown. In our co‐expression analysis, we noted that GPR21 could also form a stable complex with an unreported Gα protein subtype, Gαs. To gain further insights into the structural mechanisms of GPR21 activation, we employed cryo‐electron microscopy (cryo‐EM) and single‐particle analysis to resolve the high‐resolution structure of GPR21‐Gαs complexes. The clear electron density map of the GPR21‐Gαs provided direct evidence that GPR21 could couple to Gαs protein at physiological conditions. Thus, GPR21 might mediate previously unexplored pathways in normal or pathological conditions, which warrants further investigation. Structure‐guided mutagenesis and biochemical analysis revealed that extracellular loop 2 (ECL2) of GPR21 is essential for the receptor transducing intracellular signal via cAMP. Together, the new structure data reveal a novel signaling cascade of human GPR21 mediated by ECL2 and provide fundamental information for future structure‐based drug development.

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Cryo‐EM structure of G‐protein‐coupled receptor GPR17 in complex with inhibitory G protein

Cited by 20 publications

References 28 publications

Structural analysis of human G‐protein‐coupled receptor 17 ligand binding sites

Structural analysis of human G‐protein‐coupled receptor 17 ligand binding sites

The activation mechanism and antibody binding mode for orphan GPR20

Cryo‐EM structure of orphan G protein‐coupled receptor GPR21

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