9DQJ

CryoEM structure of Gq-coupled MRGPRD with a new agonist EP-3945


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas246Homo sapiensMutation(s): 25 
Gene Names: GNAI2GNAI2BGNASGNAS1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P04899 (Homo sapiens)
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Go to UniProtKB:  P04899
PHAROS:  P04899
GTEx:  ENSG00000114353 
Find proteins for Q5JWF2 (Homo sapiens)
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PHAROS:  Q5JWF2
GTEx:  ENSG00000087460 
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UniProt GroupsP04899Q5JWF2
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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
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Find proteins for P62873 (Homo sapiens)
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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)
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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
A1BEQ (Subject of Investigation/LOI)
Query on A1BEQ

Download Ideal Coordinates CCD File 
F [auth A]2-({1-[1-(4-methoxyphenyl)cyclopropane-1-carbonyl]piperidin-4-yl}amino)quinazolin-4(3H)-one
C24 H26 N4 O3
WAIAGNMCIITGRM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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