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- PDB-9wng: 5HT2BR-fab heterotrimer in complex with a novel antagonist IHCH-2330 -

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Basic information

Entry
Database: PDB / ID: 9wng
Title5HT2BR-fab heterotrimer in complex with a novel antagonist IHCH-2330
Components
  • 5-hydroxytryptamine receptor 2B
  • P2C2 Fab heavy chain
  • P2C2 Fab light chain
KeywordsMEMBRANE PROTEIN / GPCR / serotonin receptor / 5HT2BR
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 / phospholipase C-activating serotonin receptor signaling pathway / embryonic morphogenesis / Serotonin receptors ...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 / phospholipase C-activating serotonin receptor signaling pathway / embryonic morphogenesis / Serotonin receptors / vasoconstriction / G protein-coupled serotonin receptor activity / serotonin receptor signaling pathway / neural crest cell migration / neurotransmitter receptor activity / cardiac muscle hypertrophy / serotonin binding / neural crest cell differentiation / 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 / positive regulation of cytokine production / GTPase activator activity / 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: 2.98 Å
AuthorsTang, L. / Ji, Y. / Cheng, J. / Wang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Mechanistic Basis for 5-HT2AR Over 5-HT2BR Activation
Authors: Tang, L. / Ji, X. / Cao, D. / Li, H. / Cheng, J. / Wang, S.
History
DepositionSep 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 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
B: P2C2 Fab light chain
C: P2C2 Fab heavy chain
R: 5-hydroxytryptamine receptor 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0235
Polymers89,3523
Non-polymers6712
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: Antibody P2C2 Fab light chain


Mass: 25687.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia (bacteria)
#2: Antibody P2C2 Fab heavy chain


Mass: 29321.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia (bacteria)
#3: Protein 5-hydroxytryptamine receptor 2B / 5-HT-2B / 5-HT2B / Serotonin receptor 2B


Mass: 34342.711 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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical ChemComp-A1EXY / 3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-amino]ethyl]-2-methyl-pyrido[1,2-a]pyrimidin-4-one


Mass: 449.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26F3N3O3 / 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-2330 in complex with a Fab P2C2 obtained by cryo-electron microscopy (cryoEM)
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
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)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13CCP4 package3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 457517 / Symmetry type: POINT

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