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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9JGK

This is version 1.1 of the entry. See complete history.

Literature

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

Kaixuan, G., Xin, Z., Xiangyu, L.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41595
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EB7 (Subject of Investigation/LOI) Query on A1EB7 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Balovaptan C₂₂ H₂₄ Cl N₅ O GMPZPHGHNDMRKL-RZDIXWSQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.