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- PDB-9jgk: cryo-EM structure of 5-Hydroxytryptamine 2B Receptor in complex w... -

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Basic information

Entry
Database: PDB / ID: 9jgk
Titlecryo-EM structure of 5-Hydroxytryptamine 2B Receptor in complex with balovaptan
ComponentsSoluble cytochrome b562,5-hydroxytryptamine receptor 2B,Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,de novo design fusion protein
KeywordsMEMBRANE PROTEIN / GPCR / inactive-state / de novo protein
Function / homology
Function and homology information


intestine smooth muscle contraction / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / regulation of behavior / phospholipase C-activating serotonin receptor signaling pathway / Serotonin receptors / serotonin receptor activity / G protein-coupled serotonin receptor activity ...intestine smooth muscle contraction / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / regulation of behavior / phospholipase C-activating serotonin receptor signaling pathway / Serotonin receptors / serotonin receptor activity / G protein-coupled serotonin receptor activity / embryonic morphogenesis / serotonin receptor signaling pathway / vasoconstriction / neurotransmitter receptor activity / serotonin binding / cardiac muscle hypertrophy / neural crest cell migration / neural crest cell differentiation / : / positive regulation of cell division / G-protein alpha-subunit binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / heart morphogenesis / positive regulation of endothelial cell proliferation / ERK1 and ERK2 cascade / release of sequestered calcium ion into cytosol / GTPase activator activity / positive regulation of cytokine production / calcium-mediated signaling / electron transport chain / intracellular calcium ion homeostasis / G alpha (q) signalling events / chemical synaptic transmission / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / G protein-coupled receptor signaling pathway / iron ion binding / response to xenobiotic stimulus / positive regulation of cell population proliferation / heme binding / synapse / dendrite / negative regulation of apoptotic process / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
5-Hydroxytryptamine 2B receptor / 5-hydroxytryptamine receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
: / Soluble cytochrome b562 / 5-hydroxytryptamine receptor 2B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGao, K. / Zhang, X. / Liu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81974236 China
CitationJournal: To Be Published
Title: cryo-EM structure of 5-Hydroxytryptamine 2B Receptor in complex with balovaptan
Authors: Kaixuan, G. / Xin, Z. / Xiangyu, L.
History
DepositionSep 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / em_admin ...chem_comp / em_admin / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _em_admin.last_update / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Experimental summary / Structure summary / Data content type: EM metadata / EM metadata / Category: em_admin / entity
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _em_admin.last_update / _entity.pdbx_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,de novo design fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8132
Polymers63,4031
Non-polymers4101
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,de novo design fusion protein / Cytochrome b-562 / 5-HT-2B / 5-HT2B / Serotonin receptor 2B


Mass: 63403.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: cybC, HTR2B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7, UniProt: P41595
#2: Chemical ChemComp-A1EB7 / Balovaptan / 8-chloranyl-5-methyl-1-(4-pyridin-2-yloxycyclohexyl)-4,6-dihydro-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine


Mass: 409.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24ClN5O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 5-Hydroxytryptamine 2B Receptor/de novo design fusion protein
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Escherichia coli (E. coli)562
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TITAN THEMIS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 291656 / Symmetry type: POINT

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