8HJ5

Cryo-EM structure of Gq-coupled MRGPRX1 bound with Compound-16


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of agonist-induced activation of the human itch receptor MRGPRX1.

Gan, B.Yu, L.Yang, H.Jiao, H.Pang, B.Chen, Y.Wang, C.Lv, R.Hu, H.Cao, Z.Ren, R.

(2023) PLoS Biol 21: e3001975-e3001975

  • DOI: https://doi.org/10.1371/journal.pbio.3001975
  • Primary Citation of Related Structures:  
    8HJ5

  • PubMed Abstract: 

    Mas-related G-protein-coupled receptors X1-X4 (MRGPRX1-X4) are 4 primate-specific receptors that are recently reported to be responsible for many biological processes, including itch sensation, pain transmission, and inflammatory reactions. MRGPRX1 is the first identified human MRGPR, and its expression is restricted to primary sensory neurons. Due to its dual roles in itch and pain signaling pathways, MRGPRX1 has been regarded as a promising target for itch remission and pain inhibition. Here, we reported a cryo-electron microscopy (cryo-EM) structure of Gq-coupled MRGPRX1 in complex with a synthetic agonist compound 16 in an active conformation at an overall resolution of 3.0 Å via a NanoBiT tethering strategy. Compound 16 is a new pain-relieving compound with high potency and selectivity to MRGPRX1 over other MRGPRXs and opioid receptor. MRGPRX1 was revealed to share common structural features of the Gq-mediated receptor activation mechanism of MRGPRX family members, but the variable residues in orthosteric pocket of MRGPRX1 exhibit the unique agonist recognition pattern, potentially facilitating to design MRGPRX1-specific modulators. Together with receptor activation and itch behavior evaluation assays, our study provides a structural snapshot to modify therapeutic molecules for itch relieving and analgesia targeting MRGPRX1.


  • Organizational Affiliation

    Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(q) subunit alpha362Homo sapiensMutation(s): 0 
Gene Names: GNAI1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1384Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth D]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16D [auth C]259Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Mas-related G-protein coupled receptor member X1,LgBitE [auth F]637Escherichia coliHomo sapiensMutation(s): 3 
Gene Names: cybCMRGPRX1MRGX1SNSR3SNSR4
Membrane Entity: Yes 
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Go to UniProtKB:  P0ABE7
Find proteins for Q96LB2 (Homo sapiens)
Explore Q96LB2 
Go to UniProtKB:  Q96LB2
PHAROS:  Q96LB2
GTEx:  ENSG00000170255 
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UniProt GroupsP0ABE7Q96LB2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nb35F [auth E]157Vicugna pacosMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U2U (Subject of Investigation/LOI)
Query on U2U

Download Ideal Coordinates CCD File 
G [auth F]N-{2-[(1-aminoisoquinolin-6-yl)oxy]-4-methylphenyl}-2-methoxybenzene-1-sulfonamide
C23 H21 N3 O4 S
BWEJNHRMGZUMNU-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
U2U BindingDB:  8HJ5 EC50: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary