7Y15

Cryo-EM structure of apo-state MrgD-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein revealed by cryo-EM.

Suzuki, S.Iida, M.Hiroaki, Y.Tanaka, K.Kawamoto, A.Kato, T.Oshima, A.

(2022) Commun Biol 5: 707-707

  • DOI: https://doi.org/10.1038/s42003-022-03668-3
  • Primary Citation of Related Structures:  
    7Y12, 7Y13, 7Y14, 7Y15

  • PubMed Abstract: 

    MrgD, a member of the Mas-related G protein-coupled receptor (MRGPR) family, has high basal activity for Gi activation. It recognizes endogenous ligands, such as β-alanine, and is involved in pain and itch signaling. The lack of a high-resolution structure for MrgD hinders our understanding of whether its activation is ligand-dependent or constitutive. Here, we report two cryo-EM structures of the MrgD-Gi complex in the β-alanine-bound and apo states at 3.1 Å and 2.8 Å resolution, respectively. These structures show that β-alanine is bound to a shallow pocket at the extracellular domains. The extracellular half of the sixth transmembrane helix undergoes a significant movement and is tightly packed into the third transmembrane helix through hydrophobic residues, creating the active form. Our structures demonstrate a structural basis for the characteristic ligand recognition of MrgD. These findings provide a framework to guide drug designs targeting the MrgD receptor.


  • Organizational Affiliation

    Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.


Macromolecules
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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 
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Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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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-1356Mus musculusMutation(s): 0 
Gene Names: Gnb1
UniProt & NIH Common Fund Data Resources
Find proteins for P62874 (Mus musculus)
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Go to UniProtKB:  P62874
IMPC:  MGI:95781
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Mus musculusMutation(s): 0 
Gene Names: Gng2
Membrane Entity: Yes 
UniProt
Find proteins for P63213 (Mus musculus)
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UniProt GroupP63213
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Mas-related G-protein coupled receptor member DD [auth R]446Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 2 
Gene Names: cybCMRGPRDMRGD
Membrane Entity: Yes 
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Find proteins for P0ABE7 (Escherichia coli)
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Find proteins for Q8TDS7 (Homo sapiens)
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GTEx:  ENSG00000172938 
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UniProt GroupsP0ABE7Q8TDS7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFV16E [auth S]296synthetic constructMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP19H03165
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101074

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary