8ZWG | pdb_00008zwg

cryoEM structure of JR14a bound C3aR-Gi complex

• PDB DOI: https://doi.org/10.2210/pdb8ZWG/pdb
• EM Map EMD-60526: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Rattus norvegicus, synthetic construct, Bos taurus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-06-13 Released: 2025-05-14 
• Deposition Author(s): Luo, P., Xu, Y., Xu, H.E.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into the agonist activity of the nonpeptide modulator JR14a on C3aR.

Luo, P., Xin, W., Guo, S., Li, X., Zhang, Q., Xu, Y., He, X., Wang, Y., Fan, W., Yuan, Q., Wu, K., Hu, W., Zhuang, Y., Xu, H.E., Xie, X.

(2025) Cell Discov 11: 7-7

• PubMed: 39788969 
• DOI: https://doi.org/10.1038/s41421-024-00765-x
• Primary Citation of Related Structures:  
  8ZWF, 8ZWG

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Organizational Affiliation: 
• State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
Medicinal Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China. [e-mail].
Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research, Institute for Drug Discovery, Yantai, Shandong, China. [e-mail].

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: 176.54 kDa 
• Atom Count: 8,709 
• Modeled Residue Count: 1,121 
• Deposited Residue Count: 1,580 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2 adrenergic receptor,C3a anaphylatoxin chemotactic receptor	A	538	Homo sapiens	Mutation(s): 1  Gene Names: ADRB2, ADRB2R, B2AR, C3AR1, AZ3B, C3R1, HNFAG09
UniProt & NIH Common Fund Data Resources
Find proteins for P07550 (Homo sapiens) Explore P07550  Go to UniProtKB:  P07550
PHAROS:  P07550 GTEx:  ENSG00000169252
Find proteins for Q16581 (Homo sapiens) Explore Q16581  Go to UniProtKB:  Q16581
PHAROS:  Q16581 GTEx:  ENSG00000171860
UniProt Groups	Q16581P07550

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	354	Homo sapiens	Mutation(s): 2  Gene Names: GNAI1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	353	Rattus norvegicus	Mutation(s): 0  Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311  Go to UniProtKB:  P54311

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	D [auth E]	267	synthetic construct	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth G]	68	Bos taurus	Mutation(s): 0  Gene Names: GNG2
UniProt
Find proteins for A0A1S3WMS4 (Erinaceus europaeus) Explore A0A1S3WMS4  Go to UniProtKB:  A0A1S3WMS4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D9A (Subject of Investigation/LOI)	F [auth A]	(2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-methyl-thiophen-2-yl]carbonylamino]pentanoic acid C25 H26 Cl2 N4 O3 S OHRIKWUZKGNQKQ-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Luo, P., Xu, Y., Xu, H.E.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82121005
National Natural Science Foundation of China (NSFC)	China	32130022

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release