9DQH

CryoEM structure of Gq-coupled MRGPRD with a new agonist EP-2825


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

High-affinity agonists reveal recognition motifs for the MRGPRD GPCR.

Wang, C.Liu, Y.Lanier, M.Yeager, A.Singh, I.Gumpper, R.H.Krumm, B.E.DeLeon, C.Zhang, S.Boehm, M.Pittner, R.Baron, A.Dvorak, L.Bacon, C.Shoichet, B.K.Martinborough, E.Fay, J.F.Cao, C.Roth, B.L.

(2024) Cell Rep 43: 114942-114942

  • DOI: https://doi.org/10.1016/j.celrep.2024.114942
  • Primary Citation of Related Structures:  
    9DQH, 9DQJ

  • PubMed Abstract: 

    The human MRGPRD protein is a member of the Mas-related G protein-coupled receptors (MRGPRs) that is involved in the sensing of pain, itch, and other inflammatory stimuli. As with other MRGPRs, MRGPRD is a relatively understudied receptor with few known agonists. The most potent small-molecule agonist of MRGPRD reported so far is β-alanine, with an affinity in the micromole range, which largely restricts its functional study. Here, we report two MRGPRD agonists, EP-2825 and EP-3945, that are approximately 100-fold more potent than β-alanine and determine the structures of MRGPRD-Gq in complex with EP-2825 and EP-3945, respectively. The structures reveal distinct agonist binding modes of MRGPRD and large conformational plasticity of the orthosteric pocket. Collectively, the discovery of high-affinity MRGPRD agonists and their distinct binding modes will facilitate the functional study and the structure-based design of ligands targeting this understudied receptor.


  • Organizational Affiliation

    Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; Insitute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mas-related G-protein coupled receptor member D322Homo sapiensMutation(s): 0 
Gene Names: MRGPRDMRGD
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDS7 (Homo sapiens)
Explore Q8TDS7 
Go to UniProtKB:  Q8TDS7
GTEx:  ENSG00000172938 
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UniProt GroupQ8TDS7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gs-mini-Gq chimera246Homo sapiensMutation(s): 0 
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Entity ID: 3
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 
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UniProt GroupP62873
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
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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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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16257Mus musculusMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BE2 (Subject of Investigation/LOI)
Query on A1BE2

Download Ideal Coordinates CCD File 
F [auth A]2-({1-[2-(4-chlorophenyl)-2-methylpropanoyl]piperidin-4-yl}amino)-5,6,7,8-tetrahydroquinazolin-4(3H)-one
C23 H29 Cl N4 O2
PESFZHBYDNVCKA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DA055656
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesU24DK116195

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release