8X2K | pdb_00008x2k

OEA bound GPR3-Gs complex structure

• PDB DOI: https://doi.org/10.2210/pdb8X2K/pdb
• EM Map EMD-38015: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2023-11-09 Released: 2024-04-03 
• Deposition Author(s): Geng, C., Yang, D., Jun, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and functional characterization of the endogenous agonist for orphan receptor GPR3.

Chen, G., Staffen, N., Wu, Z., Xu, X., Pan, J., Inoue, A., Shi, T., Gmeiner, P., Du, Y., Xu, J.

(2024) Cell Res 34: 262-265

• PubMed: 38287118 
• DOI: https://doi.org/10.1038/s41422-023-00919-8
• Primary Citation of Related Structures:  
  8X2K

---

Organizational Affiliation: 
• Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, Chinese University of Hong Kong, Shenzhen, Guangdong, China.
Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen, Germany.
Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
Mass Spectrometry & Metabolomics Core Facility, Biomedical Research Core Facilities, Westlake University, Hangzhou, Zhejiang, China.
Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen, Germany. [e-mail].
Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, Chinese University of Hong Kong, Shenzhen, Guangdong, China. [e-mail].
Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, Chinese University of Hong Kong, Shenzhen, Guangdong, China. [e-mail].
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 169 kDa 
• Atom Count: 8,570 
• Modeled Residue Count: 1,111 
• Deposited Residue Count: 1,528 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,G-protein coupled receptor 3	A	466	Homo sapiens	Mutation(s): 0  Gene Names: cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P46089 (Homo sapiens) Explore P46089  Go to UniProtKB:  P46089
PHAROS:  P46089 GTEx:  ENSG00000181773
UniProt Groups	P46089P0ABE7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	B	373	Homo sapiens	Mutation(s): 0  Gene Names: GNAS, GNAS1, GSP EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens) Explore P63092  Go to UniProtKB:  P63092
PHAROS:  P63092 GTEx:  ENSG00000087460

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	357	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	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
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	261	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5YM (Subject of Investigation/LOI)	F [auth A]	(Z)-N-(2-hydroxyethyl)octadec-9-enamide C20 H39 N O2 BOWVQLFMWHZBEF-KTKRTIGZSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Geng, C., Yang, D., Jun, X.

---

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

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release
  
• Version 1.1: 2024-10-02
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-10-09
  Changes: Data collection, Structure summary