8K4S | pdb_00008k4s

CryoEM structure of Gq coupled MRGPRX4 with agonist DCA-3P


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 1.3 of the entry. See complete history


Literature

Structure-guided discovery of bile acid derivatives for treating liver diseases without causing itch.

Yang, J.Zhao, T.Fan, J.Zou, H.Lan, G.Guo, F.Shi, Y.Ke, H.Yu, H.Yue, Z.Wang, X.Bai, Y.Li, S.Liu, Y.Wang, X.Chen, Y.Li, Y.Lei, X.

(2024) Cell 187: 7164-7182.e18

  • DOI: https://doi.org/10.1016/j.cell.2024.10.001
  • Primary Citation of Related Structures:  
    8K4S, 8KEX

  • PubMed Abstract: 

    Chronic itch is a debilitating symptom profoundly impacting the quality of life in patients with liver diseases like cholestasis. Activation of the human G-protein coupled receptor, MRGPRX4 (hX4), by bile acids (BAs) is implicated in promoting cholestasis itch. However, the detailed underlying mechanisms remain elusive. Here, we identified 3-sulfated BAs that are elevated in cholestatic patients with itch symptoms. We solved the cryo-EM structure of hX4-Gq in a complex with 3-phosphated deoxycholic acid (DCA-3P), a mimic of the endogenous 3-sulfated deoxycholic acid (DCA-3S). This structure revealed an unprecedented ligand-binding pocket in MRGPR family proteins, highlighting the crucial role of the 3-hydroxyl (3-OH) group on BAs in activating hX4. Guided by this structural information, we designed and developed compound 7 (C7), a BA derivative lacking the 3-OH. Notably, C7 effectively alleviates hepatic injury and fibrosis in liver disease models while significantly mitigating the itch side effects.


  • Organizational Affiliation
    • Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4,Green fluorescent proteinA [auth E]710Escherichia coliHomo sapiensAequorea victoria
This entity is chimeric
Mutation(s): 0 
Gene Names: cybCMRGPRX4MRGX4SNSR5SNSR6GFP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
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Go to UniProtKB:  P0ABE7
Find proteins for P42212 (Aequorea victoria)
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Find proteins for Q96LA9 (Homo sapiens)
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Go to UniProtKB:  Q96LA9
PHAROS:  Q96LA9
GTEx:  ENSG00000179817 
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UniProt GroupsQ96LA9P42212P0ABE7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gs-mini-Gq chimeraB [auth A]246Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A590UJY2 (Homo sapiens)
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Go to UniProtKB:  A0A590UJY2
GTEx:  ENSG00000087460 
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UniProt GroupA0A590UJY2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]340Homo 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-2D [auth C]80Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16E [auth D]254Mus musculusMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JW0 (Subject of Investigation/LOI)
Query on JW0

Download Ideal Coordinates CCD File 
F [auth E](4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},12~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-12-oxidanyl-3-phosphonooxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic acid
C24 H41 O7 P
RDWXGGGYXLRLFX-LLQZFEROSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

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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: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-27
    Changes: Data collection
  • Version 1.3: 2024-12-25
    Changes: Data collection, Database references