9LMP | pdb_00009lmp

Cryo-EM structure of antagonist-bounded inactive human GPR4

• PDB DOI: https://doi.org/10.2210/pdb9LMP/pdb
• EM Map EMD-63220: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2025-01-19 Released: 2025-07-02 
• Deposition Author(s): Chen, L.N., Zhou, H., Xi, K., Cheng, S.Z., Liu, Y.F., Fu, Y.F., Ma, X.Y., Xu, P., Ji, S.Y., Wang, W.W., Shen, D.D., Zhang, H.B., Shen, Q.Y., Chai, R., Zhang, M., Yang, L., Han, F., Mao, C.Y., Cai, X.J., Zhang, Y.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.65 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of antagonist-bounded inactive human GPR4

Chen, L.N., Zhou, H., Xi, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 101.29 kDa 
• Atom Count: 6,224 
• Modeled Residue Count: 808 
• Deposited Residue Count: 913 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of anti-Bril Fab	A [auth H]	235	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of anti-Bril Fab	B [auth L]	216	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor 4,Soluble cytochrome b562	C [auth R]	462	Homo sapiens	Mutation(s): 0  Gene Names: GPR4, cybC
UniProt & NIH Common Fund Data Resources
Find proteins for P46093 (Homo sapiens) Explore P46093  Go to UniProtKB:  P46093
PHAROS:  P46093 GTEx:  ENSG00000177464

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L1E (Subject of Investigation/LOI)	D [auth R]	NE52-QQ57 C24 H28 N6 O HXPQWNPLNIEJOW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.65 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Chen, L.N., Zhou, H., Xi, K., Cheng, S.Z., Liu, Y.F., Fu, Y.F., Ma, X.Y., Xu, P., Ji, S.Y., Wang, W.W., Shen, D.D., Zhang, H.B., Shen, Q.Y., Chai, R., Zhang, M., Yang, L., Han, F., Mao, C.Y., Cai, X.J., Zhang, Y.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release
  
• Version 1.1: 2025-07-16
  Changes: Data collection, Structure summary