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- EMDB-0225: Mouse serotonin 5-HT3 receptor, serotonin-bound, F conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-0225
TitleMouse serotonin 5-HT3 receptor, serotonin-bound, F conformation
Map dataMouse serotonin 5-HT3 receptor, serotonin-bound, F conformation
Sample
  • Complex: 5-HT3 receptor, serotonin-bound
    • Protein or peptide: 5-hydroxytryptamine receptor 3A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SEROTONIN
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / serotonin-gated monoatomic cation channel activity / serotonin-activated cation-selective channel complex / serotonin receptor signaling pathway / serotonin binding / acetylcholine-gated monoatomic cation-selective channel activity / inorganic cation transmembrane transport / cleavage furrow / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic membrane ...Neurotransmitter receptors and postsynaptic signal transmission / serotonin-gated monoatomic cation channel activity / serotonin-activated cation-selective channel complex / serotonin receptor signaling pathway / serotonin binding / acetylcholine-gated monoatomic cation-selective channel activity / inorganic cation transmembrane transport / cleavage furrow / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic membrane / postsynaptic membrane / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / identical protein binding
Similarity search - Function
5-hydroxytryptamine 3 receptor / 5-hydroxytryptamine 3 receptor, A subunit / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain ...5-hydroxytryptamine 3 receptor / 5-hydroxytryptamine 3 receptor, A subunit / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
5-hydroxytryptamine receptor 3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPolovinkin L / Neumann E / Schoehn G / Nury H
CitationJournal: Nature / Year: 2018
Title: Conformational transitions of the serotonin 5-HT receptor.
Authors: Lucie Polovinkin / Ghérici Hassaine / Jonathan Perot / Emmanuelle Neumann / Anders A Jensen / Solène N Lefebvre / Pierre-Jean Corringer / Jacques Neyton / Christophe Chipot / Francois ...Authors: Lucie Polovinkin / Ghérici Hassaine / Jonathan Perot / Emmanuelle Neumann / Anders A Jensen / Solène N Lefebvre / Pierre-Jean Corringer / Jacques Neyton / Christophe Chipot / Francois Dehez / Guy Schoehn / Hugues Nury /
Abstract: The serotonin 5-HT receptor is a pentameric ligand-gated ion channel (pLGIC). It belongs to a large family of receptors that function as allosteric signal transducers across the plasma membrane; upon ...The serotonin 5-HT receptor is a pentameric ligand-gated ion channel (pLGIC). It belongs to a large family of receptors that function as allosteric signal transducers across the plasma membrane; upon binding of neurotransmitter molecules to extracellular sites, the receptors undergo complex conformational transitions that result in transient opening of a pore permeable to ions. 5-HT receptors are therapeutic targets for emesis and nausea, irritable bowel syndrome and depression. In spite of several reported pLGIC structures, no clear unifying view has emerged on the conformational transitions involved in channel gating. Here we report four cryo-electron microscopy structures of the full-length mouse 5-HT receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator, at resolutions ranging from 3.2 Å to 4.5 Å. The tropisetron-bound structure resembles those obtained with an inhibitory nanobody or without ligand. The other structures include an 'open' state and two ligand-bound states. We present computational insights into the dynamics of the structures, their pore hydration and free-energy profiles, and characterize movements at the gate level and cation accessibility in the pore. Together, these data deepen our understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.
History
DepositionAug 30, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseNov 7, 2018-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hin
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0225.png

Downloads & links

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Map

FileDownload / File: emd_0225.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMouse serotonin 5-HT3 receptor, serotonin-bound, F conformation
Voxel sizeX=Y=Z: 1.039 Å
Density
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-21.660654 - 32.166874
Average (Standard dev.)2.4984789e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0391.0391.039
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z249.360249.360249.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-21.66132.1670.000

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Supplemental data

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Sample components

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Entire : 5-HT3 receptor, serotonin-bound

EntireName: 5-HT3 receptor, serotonin-bound
Components
  • Complex: 5-HT3 receptor, serotonin-bound
    • Protein or peptide: 5-hydroxytryptamine receptor 3A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SEROTONIN

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Supramolecule #1: 5-HT3 receptor, serotonin-bound

SupramoleculeName: 5-HT3 receptor, serotonin-bound / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293

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Macromolecule #1: 5-hydroxytryptamine receptor 3A

MacromoleculeName: 5-hydroxytryptamine receptor 3A / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 51.906031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PALLRLSDHL LANYKKGVRP VRDWRKPTTV SIDVIMYAIL NVDEKNQVLT TYIWYRQYWT DEFLQWTPED FDNVTKLSIP TDSIWVPDI LINEFVDVGK SPNIPYVYVH HRGEVQNYKP LQLVTACSLD IYNFPFDVQN CSLTFTSWLH TIQDINITLW R SPEEVRSD ...String:
PALLRLSDHL LANYKKGVRP VRDWRKPTTV SIDVIMYAIL NVDEKNQVLT TYIWYRQYWT DEFLQWTPED FDNVTKLSIP TDSIWVPDI LINEFVDVGK SPNIPYVYVH HRGEVQNYKP LQLVTACSLD IYNFPFDVQN CSLTFTSWLH TIQDINITLW R SPEEVRSD KSIFINQGEW ELLEVFPQFK EFSIDISNSY AEMKFYVIIR RRPLFYAVSL LLPSIFLMVV DIVGFCLPPD SG ERVSFKI TLLLGYSVFL IIVSDTLPAT AIGTPLIGVY FVVCMALLVI SLAETIFIVR LVHKQDLQRP VPDWLRHLVL DRI AWILCL GEQPMAHRPP ATFQANKTDD CSGSDLLPAM GNHCSHVGGP QDLEKTPRGR GSPLPPPREA SLAVRGLLQE LSSI RHFLE KRDEMREVAR DWLRVGYVLD RLLFRIYLLA VLAYSITLVT LWSIW

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #4: SEROTONIN

MacromoleculeName: SEROTONIN / type: ligand / ID: 4 / Number of copies: 5 / Formula: SRO
Molecular weightTheoretical: 176.215 Da
Chemical component information

ChemComp-SRO:
SEROTONIN / neurotransmitter*YM / Serotonin

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4pir

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10667

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