9IYA | pdb_00009iya

Cryo-EM structure of GPR55-Fab-Nb-ONO-9710531 complex

• PDB DOI: https://doi.org/10.2210/pdb9IYA/pdb
• EM Map EMD-60993: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-07-30 Released: 2025-01-01 
• Deposition Author(s): Hua, T., Liu, Z.J., Cherezov, V., Chang, H., Li, X.T., Shen, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure basis of ligand recognition and activation of GPR55.

Chang, H., Li, X., Shen, L., Ge, X., Hao, S., Wu, L., Liu, S., Liu, J., Cherezov, V., Hua, T.

(2025) Cell Res 35: 80-83

• PubMed: 39482405 
• DOI: https://doi.org/10.1038/s41422-024-01046-8
• Primary Citation of Related Structures:  
  9IY8, 9IYA

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Bridge Institute, University of Southern California, Los Angeles, CA, USA.
Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
Bridge Institute, University of Southern California, Los Angeles, CA, USA. [e-mail].
Department of Chemistry, University of Southern California, Los Angeles, CA, USA. [e-mail].
iHuman Institute, ShanghaiTech University, Shanghai, 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 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 110.63 kDa 
• Atom Count: 7,219 
• Modeled Residue Count: 924 
• Deposited Residue Count: 996 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor 55,Soluble cytochrome b562	A	412	Homo sapiens	Mutation(s): 0  Gene Names: GPR55, 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 Q9Y2T6 (Homo sapiens) Explore Q9Y2T6  Go to UniProtKB:  Q9Y2T6
PHAROS:  Q9Y2T6 GTEx:  ENSG00000135898
UniProt Groups	Q9Y2T6P0ABE7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-BRIL Fab Heavy chain	B [auth H]	246	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-BRIL Fab Light chain	C [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-Fab Nanobody	D [auth N]	123	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L3E (Subject of Investigation/LOI)	E [auth A]	4-(3-bromanyl-5-ethoxy-4-oxidanyl-phenyl)-~{N}-(2-methoxyphenyl)-2-methyl-5-oxidanylidene-4,6,7,8-tetrahydro-1~{H}-quinoline-3-carboxamide C26 H27 Br N2 O5 VFIAGZFUJFJECK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Hua, T., Liu, Z.J., Cherezov, V., Chang, H., Li, X.T., Shen, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	91953202

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Data collection, Database references