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 23CY | pdb_000023cy

Cryo-EM structure of the MRGPRX4-miniGsq complex bound to the inverse agonist cmpd54-4, local


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 23CY

This is version 1.1 of the entry. See complete history. 

Literature

Structural insights into the ligand modulation of MRGPRX4 conformational plasticity.

Zhang, M., Wang, Y., Huang, Y., Liang, Y., Chen, P., Ji, Z., Song, M., Chen, H., Wang, C., Cao, C.

(2026) Cell Discov 12

  • DOI: https://doi.org/10.1038/s41421-026-00929-x
  • Primary Citation Related Structures: 
    23CS, 23CU, 23CV, 23CW, 23CX, 23CY

  • PubMed Abstract: 

    Chronic pruritus is a debilitating condition with limited treatment options, particularly in cholestatic liver diseases, where bile acid dysregulation is a known trigger. Although Mas-related G protein-coupled receptor X4 (MRGPRX4) has recently been identified as a key mediator of bile acid-induced pruritus, the structural mechanisms underlying its inhibition remain poorly understood, hindering the development of therapeutic antagonists. Here, we report the cryo-electron microscopy structures of MRGPRX4 in three distinct states: agonist-bound state, antagonist-bound state, and apo state. Our structures reveal a previously unrecognized antagonist-binding site that is structurally distinct from those engaged by agonists. Complementary functional assays and molecular dynamics simulations further demonstrate that the extracellular pocket of MRGPRX4 undergoes pronounced ligand-dependent conformational rearrangements upon binding to both the agonist and the antagonist. Collectively, these findings elucidate the conformational plasticity underlying MRGPRX4 activity modulation and establish a structural framework for the rational design of MRGPRX4 antagonists that target chronic pruritus.


  • Organizational Affiliation: 
    • Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.

Macromolecule Content 

  • Total Structure Weight: 53.8 kDa 
  • Atom Count: 1,907 
  • Modeled Residue Count: 244 
  • Deposited Residue Count: 472 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4472Escherichia coli, Homo sapiens
This entity is chimeric
Mutation(s): 1 
Gene Names: cybC, MRGPRX4, MRGX4, SNSR5, SNSR6
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q96LA9 (Homo sapiens)
Explore Q96LA9 
Go to UniProtKB:  Q96LA9
PHAROS:  Q96LA9
GTEx:  ENSG00000179817 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7Q96LA9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1E43
(Subject of Investigation/LOI)

Query on A1E43



Download:Ideal Coordinates CCD File
B [auth A](2~{S})-2-[[3-[[2-chloranyl-4-(trifluoromethyl)phenoxy]methyl]phenyl]carbonylamino]propanoic acid
C18 H15 Cl F3 N O4
SJHHZIPCIDRJQR-JTQLQIEISA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2025YFA1309100
National Natural Science Foundation of China (NSFC)China82504820

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-14
    Type: Initial release
  • Version 1.1: 2026-11-04
    Changes: Data collection, Database references