9JGK | pdb_00009jgk

cryo-EM structure of 5-Hydroxytryptamine 2B Receptor in complex with balovaptan

• PDB DOI: https://doi.org/10.2210/pdb9JGK/pdb
• EM Map EMD-61466: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli, Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-09-07 Released: 2025-07-16 
• Deposition Author(s): Gao, K., Zhang, X., Liu, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

cryo-EM structure of 5-Hydroxytryptamine 2B Receptor in complex with balovaptan

Kaixuan, G., Xin, Z., Xiangyu, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 63.81 kDa 
• Atom Count: 2,606 
• Modeled Residue Count: 374 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,de novo design fusion protein	A	568	Escherichia coli, Homo sapiens, synthetic construct	Mutation(s): 1  Gene Names: cybC, HTR2B
UniProt & NIH Common Fund Data Resources
Find proteins for P41595 (Homo sapiens) Explore P41595  Go to UniProtKB:  P41595
PHAROS:  P41595 GTEx:  ENSG00000135914

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EB7 (Subject of Investigation/LOI)	B [auth A]	Balovaptan C22 H24 Cl N5 O GMPZPHGHNDMRKL-RZDIXWSQSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Gao, K., Zhang, X., Liu, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81974236

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release
  
• Version 1.1: 2025-11-26
  Changes: Data collection, Derived calculations, Structure summary