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- EMDB-68737: local refinement of 5HT2AR-miniGq heterotrimer in complex with a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-68737
Titlelocal refinement of 5HT2AR-miniGq heterotrimer in complex with a selective agonist IHCH-2330
Map data
Sample
  • Complex: local refinement of 5-HT2A receptor bound to IHCH-2330 in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)
    • Protein or peptide: 5-hydroxytryptamine receptor 2A
  • 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 / 5HT2AR
Function / homology
Function and homology information


positive regulation of heat generation / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / serotonin receptor activity / 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 / neurofilament / cell body fiber / artery smooth muscle contraction ...positive regulation of heat generation / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / serotonin receptor activity / 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 / neurofilament / cell body fiber / artery smooth muscle contraction / positive regulation of cytokine production involved in immune response / sensitization / Serotonin receptors / phospholipase C-activating serotonin receptor signaling pathway / G protein-coupled serotonin receptor activity / serotonin receptor signaling pathway / urinary bladder smooth muscle contraction / serotonin binding / positive regulation of platelet aggregation / neurotransmitter receptor activity / negative regulation of synaptic transmission, glutamatergic / positive regulation of DNA biosynthetic process / temperature homeostasis / negative regulation of potassium ion transport / detection of temperature stimulus involved in sensory perception of pain / regulation of dopamine secretion / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of vasoconstriction / positive regulation of execution phase of apoptosis / protein tyrosine kinase activator activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / release of sequestered calcium ion into cytosol / behavioral response to cocaine / presynaptic modulation of chemical synaptic transmission / dendritic shaft / memory / caveola / intracellular calcium ion homeostasis / virus receptor activity / positive regulation of neuron apoptotic process / positive regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / chemical synaptic transmission / presynaptic membrane / G alpha (q) signalling events / positive regulation of ERK1 and ERK2 cascade / postsynaptic membrane / response to xenobiotic stimulus / axon / neuronal cell body / positive regulation of cell population proliferation / dendrite / protein-containing complex binding / glutamatergic synapse / identical protein binding / plasma membrane
Similarity search - Function
5-Hydroxytryptamine 2A 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 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTang L / Ji X / Cheng J / Wang S
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Chinese Academy of Sciences China
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Mechanistic Basis for 5-HT2AR Over 5-HT2BR Activation
Authors: Tang L / Ji X / Wang Y / Cao D / Li H / He L / Cheng J / Wang S
History
DepositionJan 26, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68737.png

Downloads & links

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Map

FileDownload / File: emd_68737.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 256 pix.
= 232.96 Å		0.91 Å/pix.
x 256 pix.
= 232.96 Å		0.91 Å/pix.
x 256 pix.
= 232.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-1.3768678 - 1.8173497
Average (Standard dev.)-0.00088753557 (±0.031115206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 232.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68737_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68737_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : local refinement of 5-HT2A receptor bound to IHCH-2330 in complex...

EntireName: local refinement of 5-HT2A receptor bound to IHCH-2330 in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)
Components
  • Complex: local refinement of 5-HT2A receptor bound to IHCH-2330 in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)
    • Protein or peptide: 5-hydroxytryptamine receptor 2A
  • 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: local refinement of 5-HT2A receptor bound to IHCH-2330 in complex...

SupramoleculeName: local refinement of 5-HT2A receptor bound to IHCH-2330 in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 5-hydroxytryptamine receptor 2A

MacromoleculeName: 5-hydroxytryptamine receptor 2A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.50727 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGSGSGLSL LHLQEKNWSA LLTAVVIILT IAGNILVIMA VSLEKKLQNA TNYFLMSLAI ADMLLGFLVM PVSMLTILYG YRWPLPSKL CAVWIYLDVL FSTASIMHLC AISLDRYVAI QNPIHHSRFN SRTKAFLKII AVWTISVGIS MPIPVFGLQD D SKVFKEGS ...String:
GPGSGSGLSL LHLQEKNWSA LLTAVVIILT IAGNILVIMA VSLEKKLQNA TNYFLMSLAI ADMLLGFLVM PVSMLTILYG YRWPLPSKL CAVWIYLDVL FSTASIMHLC AISLDRYVAI QNPIHHSRFN SRTKAFLKII AVWTISVGIS MPIPVFGLQD D SKVFKEGS CLLADDNFVL IGSFVSFFIP LTIMVITYFL TIKSLQKEAT LCVSDLGTRA KLASFSFLPQ SSLSSEKLFQ RS IHREPGS YTGRRTMQSI SNEQKACKVL GIVFFLFVVM WCPFFITNIM AVICKESCNE DVIGALLNVF VWIGYLSSAV NPL VYTLFN KTYRSAFSRY

UniProtKB: 5-hydroxytryptamine receptor 2A

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Macromolecule #2: 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: 2 / 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:

7ran

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: CCP4 package / Number images used: 186920
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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