8K4S

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

• PDB DOI: https://doi.org/10.2210/pdb8K4S/pdb
• EM Map EMD-36890: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli, Homo sapiens, Aequorea victoria, Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-07-20 Released: 2024-11-06 
• Deposition Author(s): Yang, J., Fan, J.P., Lei, X.G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

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

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 

• DOI: https://doi.org/10.1016/j.cell.2024.10.001

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 181.16 kDa 
• Atom Count: 8,196 
• Modelled Residue Count: 1,093 
• Deposited Residue Count: 1,630 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4,Green fluorescent protein	A [auth E]	710	Escherichia coli, Homo sapiens, Aequorea victoria This entity is chimeric	Mutation(s): 0  Gene Names: cybC, MRGPRX4, MRGX4, SNSR5, SNSR6, GFP
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
Find proteins for Q96LA9 (Homo sapiens) Explore Q96LA9  Go to UniProtKB:  Q96LA9
PHAROS:  Q96LA9 GTEx:  ENSG00000179817
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
UniProt Groups	Q96LA9P42212P0ABE7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gs-mini-Gq chimera	B [auth A]	246	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C [auth B]	340	Homo sapiens	Mutation(s): 0  Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
PHAROS:  P62873 GTEx:  ENSG00000078369

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D [auth C]	80	Homo sapiens	Mutation(s): 0  Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	E [auth D]	254	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JW0 (Subject of Investigation/LOI)	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

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Yang, J., Fan, J.P., Lei, X.G.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release