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- PDB-9wqa: 5-HT2B receptor bound to IHCH-1906 in complex with an antibody ob... -

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Basic information

Entry
Database: PDB / ID: 9wqa
Title5-HT2B receptor bound to IHCH-1906 in complex with an antibody obtained by cryo-electron microscopy (cryoEM)
Components
  • 5-hydroxytryptamine receptor 2B
  • Anti-5-HT2B Fab heavy chain
  • Anti-5-HT2B Fab light chain
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / serotonin receptor / membrane protein / 5-HT2AR / SIGNALING PROTEIN-IMMUNE SYSTEM complex
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 / serotonin receptor activity / vasoconstriction / embryonic morphogenesis / phospholipase C-activating serotonin receptor signaling pathway ...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 / serotonin receptor activity / vasoconstriction / embryonic morphogenesis / phospholipase C-activating serotonin receptor signaling pathway / Serotonin receptors / G protein-coupled serotonin receptor activity / serotonin receptor signaling pathway / neural crest cell migration / cardiac muscle hypertrophy / serotonin binding / neural crest cell differentiation / neurotransmitter receptor activity / positive regulation of cell division / ERK1 and ERK2 cascade / heart morphogenesis / G-protein alpha-subunit binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / release of sequestered calcium ion into cytosol / positive regulation of endothelial cell proliferation / GTPase activator activity / positive regulation of cytokine production / calcium-mediated signaling / intracellular calcium ion homeostasis / chemical synaptic transmission / G alpha (q) signalling events / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / negative regulation of apoptotic process / dendrite / synapse / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
5-Hydroxytryptamine 2B receptor / 5-hydroxytryptamine receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / 5-hydroxytryptamine receptor 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsLi, H. / Tang, L. / Zhang, J. / Meng, B. / Cao, D. / Yu, J. / Liu, Z. / Wang, S. / Cheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure-based design of subtype-selective psychedelic analogues
Authors: Li, H. / Tang, J. / Zhang, J. / Meng, B. / Cao, D. / Yu, J. / Liu, Z. / Wang, S. / Cheng, J.
History
DepositionSep 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-hydroxytryptamine receptor 2B
B: Anti-5-HT2B Fab light chain
C: Anti-5-HT2B Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7634
Polymers85,5203
Non-polymers2431
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 5-hydroxytryptamine receptor 2B / 5-HT-2B / 5-HT2B / Serotonin receptor 2B


Mass: 35582.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTR2B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41595
#2: Antibody Anti-5-HT2B Fab light chain


Mass: 23151.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody Anti-5-HT2B Fab heavy chain


Mass: 26785.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Chemical ChemComp-A1EYE / 1-(1,2,3,6-tetrahydropyridin-4-yl)-6,7,8,9-tetrahydro-5~{H}-benzo[7]annulen-4-ol


Mass: 243.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21NO / 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-HT2B receptor bound to IHCH-1906 in complex with an antibody obtained by cryo-electron microscopy (cryoEM)
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 7677

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304371 / Symmetry type: POINT
RefinementHighest resolution: 3.28 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035268
ELECTRON MICROSCOPYf_angle_d0.6617198
ELECTRON MICROSCOPYf_dihedral_angle_d5.046741
ELECTRON MICROSCOPYf_chiral_restr0.043861
ELECTRON MICROSCOPYf_plane_restr0.004893

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