8XOF | pdb_00008xof

Cryo-EM structure of Lys05 bound GPR30-Gq complex structure

• PDB DOI: https://doi.org/10.2210/pdb8XOF/pdb
• EM Map EMD-38527: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-01-01 Released: 2024-04-10 
• Deposition Author(s): Liu, H., Xu, P., Xu, H.E.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and functional evidence that GPR30 is not a direct estrogen receptor.

Liu, H., Guo, S., Dai, A., Xu, P., Li, X., Huang, S., He, X., Wu, K., Zhang, X., Yang, D., Xie, X., Xu, H.E.

(2024) Cell Res 34: 530-533

• PubMed: 38744981 
• DOI: https://doi.org/10.1038/s41422-024-00963-y
• Primary Citation of Related Structures:  
  8XOF, 8XOG, 8XOH, 8XOI, 8XOJ

---

Organizational Affiliation: 
• The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
The State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
The State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
The 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].
The 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 Life Science and Technology, ShanghaiTech University, Shanghai, 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: 146.11 kDa 
• Atom Count: 8,025 
• Modeled Residue Count: 1,015 
• Deposited Residue Count: 1,296 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G protein subunit q	A	361	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	351	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody35	D [auth N]	138	Lama glama	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled estrogen receptor 1	E [auth R]	375	Homo sapiens	Mutation(s): 0  Gene Names: GPER1, CEPR, CMKRL2, DRY12, GPER, GPR30 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q99527 (Homo sapiens) Explore Q99527  Go to UniProtKB:  Q99527
PHAROS:  Q99527 GTEx:  ENSG00000164850

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LVW	F [auth R]	Lys01 C23 H23 Cl2 N5 WDGQVCRQXSYPCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Liu, H., Xu, P., Xu, H.E.

---

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

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release
  
• Version 1.1: 2024-07-03
  Changes: Data collection, Database references
• Version 1.2: 2024-07-10
  Changes: Data collection, Database references
• Version 1.3: 2024-10-09
  Changes: Data collection, Structure summary
• Version 1.4: 2025-06-18
  Changes: Data collection