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- EMDB-66117: 5HT2BR-fab heterotrimer in complex with a novel antagonist IHCH-2330 -

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Basic information

Entry
Database: EMDB / ID: EMD-66117
Title5HT2BR-fab heterotrimer in complex with a novel antagonist IHCH-2330
Map data
Sample
  • Complex: 5-HT2B receptor bound to IHCH-2330 in complex with a Fab P2C2 obtained by cryo-electron microscopy (cryoEM)
    • Protein or peptide: P2C2 Fab light chain
    • Protein or peptide: P2C2 Fab heavy chain
    • Protein or peptide: 5-hydroxytryptamine receptor 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-amino]ethyl]-2-methyl-pyrido[1,2-a]pyrimidin-4-one
KeywordsGPCR / serotonin receptor / MEMBRANE PROTEIN / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsTang L / Ji Y / Cheng J / Wang S
Funding support China, 1 items
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, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66117.png

Downloads & links

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Map

FileDownload / File: emd_66117.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 260 pix.
= 299.52 Å		1.15 Å/pix.
x 260 pix.
= 299.52 Å		1.15 Å/pix.
x 260 pix.
= 299.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.152 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-2.0822966 - 3.129474
Average (Standard dev.)-0.00027155972 (±0.042121574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 299.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66117_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66117_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 5-HT2B receptor bound to IHCH-2330 in complex with a Fab P2C2 obt...

EntireName: 5-HT2B receptor bound to IHCH-2330 in complex with a Fab P2C2 obtained by cryo-electron microscopy (cryoEM)
Components
  • Complex: 5-HT2B receptor bound to IHCH-2330 in complex with a Fab P2C2 obtained by cryo-electron microscopy (cryoEM)
    • Protein or peptide: P2C2 Fab light chain
    • Protein or peptide: P2C2 Fab heavy chain
    • Protein or peptide: 5-hydroxytryptamine receptor 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-amino]ethyl]-2-methyl-pyrido[1,2-a]pyrimidin-4-one

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Supramolecule #1: 5-HT2B receptor bound to IHCH-2330 in complex with a Fab P2C2 obt...

SupramoleculeName: 5-HT2B receptor bound to IHCH-2330 in complex with a Fab P2C2 obtained by cryo-electron microscopy (cryoEM)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: P2C2 Fab light chain

MacromoleculeName: P2C2 Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.687918 KDa
Recombinant expressionOrganism: Escherichia (bacteria)
SequenceString: MKKNIAFLLA SMFVFSIATN AYADIVLIQS PAIMSASPGE KVTITCSASS SVSYMHWFQQ KPGTSPKLWI YSTSNLASGV PARFSGSGS GTSYSLTISR MEAEDAATYY CQQRSSYPLT FGAGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV ...String:
MKKNIAFLLA SMFVFSIATN AYADIVLIQS PAIMSASPGE KVTITCSASS SVSYMHWFQQ KPGTSPKLWI YSTSNLASGV PARFSGSGS GTSYSLTISR MEAEDAATYY CQQRSSYPLT FGAGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSLPVT KSFNRGEC

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Macromolecule #2: P2C2 Fab heavy chain

MacromoleculeName: P2C2 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.321865 KDa
Recombinant expressionOrganism: Escherichia (bacteria)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAEVQLQQS GPELVKPGAS VKLSCKASGY TFTSSWMHWV KQRPGQGLEW IGNIYPSNGG TNYNERFKS KATLTVDRSS NTAYMQLSSL TSEDSAVYFC ARFGSFITTI LTTYYNPVDY WGQGTTLTVS SASTKGPSVF P LAPSSKST ...String:
MKKNIAFLLA SMFVFSIATN AYAEVQLQQS GPELVKPGAS VKLSCKASGY TFTSSWMHWV KQRPGQGLEW IGNIYPSNGG TNYNERFKS KATLTVDRSS NTAYMQLSSL TSEDSAVYFC ARFGSFITTI LTTYYNPVDY WGQGTTLTVS SASTKGPSVF P LAPSSKST SGGTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PS NTKVDKK VEPKSCENLY FQSGSHHHHH HHH

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Macromolecule #3: 5-hydroxytryptamine receptor 2B

MacromoleculeName: 5-hydroxytryptamine receptor 2B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.342711 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGSGSGTES IPEEMKQIVE EQGNKLHWAA LLILMVIIPT IGGNTLVILA VSLEKKLQYA TNYFLMSLAV ADLLVGLFVM PIALLTIMF EAMWPLPLVL CPAWLFLDVL FSTASIWHLC AISVDRYIAI KKPIQANQYN SRATAFIKIT VVWLISIGIA I PVPIKGIE ...String:
GPGSGSGTES IPEEMKQIVE EQGNKLHWAA LLILMVIIPT IGGNTLVILA VSLEKKLQYA TNYFLMSLAV ADLLVGLFVM PIALLTIMF EAMWPLPLVL CPAWLFLDVL FSTASIWHLC AISVDRYIAI KKPIQANQYN SRATAFIKIT VVWLISIGIA I PVPIKGIE TDVDNPNNIT CVLTKERFGD FMLFGSLAAF FTPLAIMIVT YFLTIHALQK KRLLSGSRQT ISNEQRASKV LG IVFFLFL LMWCPFFITN ITLVLCDSCN QTTLQMLLEI FVWIGYVSSG VNPLVYTLFN KTFRDAFGRY

UniProtKB: 5-hydroxytryptamine receptor 2B, 5-hydroxytryptamine receptor 2B

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: 3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-ami...

MacromoleculeName: 3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-amino]ethyl]-2-methyl-pyrido[1,2-a]pyrimidin-4-one
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1EXY
Molecular weightTheoretical: 449.466 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7srq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: CCP4 package / Number images used: 457517
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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