9JGK: 5-Hydroxytryptamine 2B Receptor

cryo-EM structure of 5-Hydroxytryptamine 2B Receptor in complex with balovaptan. Determined by electron microscopy at 3.6 Å resolution. Released 16 Jul 2025.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 1
Atoms: 2,606
Mol. weight: 63.81 kDa
Ligands: A1EB7
Released: 16 Jul 2025

Explore 9JGK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JGK contains 21 α-helices and 0 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 0 β-strands

Element	Residues	Length
α-helix	65-81	17
α-helix	88-106	19
α-helix	108-116	9
α-helix	125-127	3
α-helix	128-158	31
α-helix	160-163	4
α-helix	173-186	14
α-helix	215-222	8
α-helix	223-227	5
α-helix	228-254	27
α-helix	264-272	9
α-helix	285-291	7
α-helix	302-310	9
α-helix	318-329	12
α-helix	333-348	16
α-helix	353-361	9
α-helix	367-378	12
α-helix	384-425	42
α-helix	434-449	16
α-helix	450-453	4
α-helix	455-462	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,Soluble cytochrome…	A	protein	568	Escherichia coli, Homo sapiens, synthetic construct	P41595 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9JGK_1 Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,de novo design fusion protein (chains A)
DYKDDDAADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSP
DSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLTESIPEE
MKQIVEEQGNKLHWAALLILMVIIPTIGGNTLVILAVSLEKKLQYATNYFLMSLAVADLL
VGLFVMPIALLTIMFEAMWPLPLVLCPAWLFLDVLFSTASIWHLCAISVDRYIAIKKPIQ
ANQYNSRATAFIKITVVWLISIGIAIPVPIKGIETDVDNPNNITCVLTKERFGDFMLFGS
LAAFFTPLAIMIVTYFLTIRFRRRGAEALERAFSLEDDKEALLAALDALAEAFADDAELT
ALLALLRRLLEDPDLPADELAALRAALTRFPEFREALLALLDRYLATRDLADARDLVWAL
VLAIASDPRYRPAVAAMIAFGDAEVLRAGLLRGAEALGLPGGEALVEEIMAEAENEQRAS
KVLGIVFFLFLLMWCPFFITNITLVLCDSCNQTTLQMLLEIFVWIGYVSSGVNPLVYTLF
NKTFRDAFGRYITCNYRATKSVHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1EB7	Balovaptan	C22 H24 Cl N5 O	1

Primary citation

cryo-EM structure of 5-Hydroxytryptamine 2B Receptor in complex with balovaptan. Kaixuan, G., Xin, Z., Xiangyu, L. To be published.

Other PDB entries of the same protein (UniProt P41595 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4IB4 2.7 Å, Crystal structure of the chimeric protein of 5-HT2B-BRIL in complex with ergotamine
7SRQ 2.7 Å, 5-HT2B receptor bound to LSD obtained by cryo-electron microscopy (cryoEM)
4NC3 2.8 Å, Crystal structure of the 5-HT2B receptor solved using serial femtosecond crystallography…
5TVN 2.9 Å, Crystal structure of the LSD-bound 5-HT2B receptor
7SRR 2.9 Å, 5-HT2B receptor bound to LSD in complex with heterotrimeric mini-Gq protein obtained by…
6DRY 2.92 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
9WNG 2.98 Å, 5HT2BR-fab heterotrimer in complex with a novel antagonist IHCH-2330
5TUD 3.0 Å, Structural Insights into the Extracellular Recognition of the Human Serotonin 2B…
6DRX 3.1 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
6DRZ 3.1 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
9WQB 3.18 Å, 5-HT2B receptor bound to IHCH-6122 in complex with an antibody obtained by cryo-electron…
6DS0 3.19 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor

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