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- PDB-9as9: Local refinement of 5-HT2AR bound to RS130-180 in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 9as9
TitleLocal refinement of 5-HT2AR bound to RS130-180 in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM)
Components5-hydroxytryptamine receptor 2A
KeywordsMEMBRANE PROTEIN / GPCR / G-protein Coupled Receptor / 5-HT2AR / serotonin / psychedelics
Function / homology
Function and homology information


protein localization to cytoskeleton / positive regulation of heat generation / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / 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 / Serotonin receptors ...protein localization to cytoskeleton / positive regulation of heat generation / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / 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 / Serotonin receptors / serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / artery smooth muscle contraction / G protein-coupled serotonin receptor activity / positive regulation of cytokine production involved in immune response / serotonin receptor signaling pathway / sensitization / neurotransmitter receptor activity / urinary bladder smooth muscle contraction / serotonin binding / positive regulation of platelet aggregation / negative regulation of synaptic transmission, glutamatergic / positive regulation of DNA biosynthetic process / temperature homeostasis / positive regulation of vasoconstriction / regulation of dopamine secretion / detection of temperature stimulus involved in sensory perception of pain / negative regulation of potassium ion transport / protein tyrosine kinase activator activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of execution phase of apoptosis / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of fat cell differentiation / behavioral response to cocaine / release of sequestered calcium ion into cytosol / presynaptic modulation of chemical synaptic transmission / positive regulation of glycolytic process / dendritic shaft / glycolytic process / caveola / memory / intracellular calcium ion homeostasis / positive regulation of inflammatory response / positive regulation of neuron apoptotic process / presynaptic membrane / positive regulation of cytosolic calcium ion concentration / virus receptor activity / cytoplasmic vesicle / G alpha (q) signalling events / chemical synaptic transmission / postsynaptic membrane / positive regulation of ERK1 and ERK2 cascade / 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. / 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
: / 5-hydroxytryptamine receptor 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsGumpper, R.H. / Fay, J.F. / Roth, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA)HR0011-20-2-0029 United States
CitationJournal: Nat Commun / Year: 2025
Title: The structural diversity of psychedelic drug actions revealed.
Authors: Ryan H Gumpper / Manish K Jain / Kuglae Kim / Renhong Sun / Ning Sun / Zhongli Xu / Jeffrey F DiBerto / Brian E Krumm / Nicholas J Kapolka / H Ümit Kaniskan / David E Nichols / Jian Jin / ...Authors: Ryan H Gumpper / Manish K Jain / Kuglae Kim / Renhong Sun / Ning Sun / Zhongli Xu / Jeffrey F DiBerto / Brian E Krumm / Nicholas J Kapolka / H Ümit Kaniskan / David E Nichols / Jian Jin / Jonathan F Fay / Bryan L Roth /
Abstract: There is currently a resurgence in exploring the utility of classical psychedelics to treat depression, addiction, anxiety disorders, cluster headaches, and many other neuropsychiatric disorders. A ...There is currently a resurgence in exploring the utility of classical psychedelics to treat depression, addiction, anxiety disorders, cluster headaches, and many other neuropsychiatric disorders. A biological target of these compounds, and a hypothesized target for their therapeutic actions, is the 5-HT serotonin receptor. Here, we present 7 cryo-EM structures covering all major compound classes of psychedelic and non-psychedelic agonists, including a β-arrestin-biased compound RS130-180. Identifying the molecular interactions between various psychedelics and the 5-HT receptor reveals both common and distinct motifs among the examined psychedelic chemotypes. These findings lead to a broader mechanistic understanding of 5-HT activation, which can catalyze the development of novel chemotypes with potential therapeutic utility and fewer side effects.
History
DepositionFeb 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-hydroxytryptamine receptor 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0172
Polymers52,6491
Non-polymers3681
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 2A / 5-HT-2 / 5-HT-2A / Serotonin receptor 2A


Mass: 52648.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTR2A, HTR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28223
#2: Chemical ChemComp-A1AFX / 2,5-dimethoxy-N,N-dimethyl-4-{2-[({2-[(prop-2-yn-1-yl)oxy]phenyl}methyl)amino]ethyl}aniline


Mass: 368.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N2O3 / 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-HT2AR in complex with mini-Gq / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2600 nm / Nominal defocus min: 160 nm
Image recordingElectron dose: 49.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232870 / Symmetry type: POINT
RefinementHighest resolution: 3.47 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0092010
ELECTRON MICROSCOPYf_angle_d1.0892752
ELECTRON MICROSCOPYf_dihedral_angle_d10.931279
ELECTRON MICROSCOPYf_chiral_restr0.044345
ELECTRON MICROSCOPYf_plane_restr0.012329

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