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- EMDB-15471: Mouse serotonin 5-HT3A receptor in amphipols A8-35 -

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Basic information

Entry
Database: EMDB / ID: EMD-15471
TitleMouse serotonin 5-HT3A receptor in amphipols A8-35
Map datam5HT3A receptor in A8-35 amphipols
Sample
  • Complex: Homopentameric complex of 5-HT3A receptor subunits
    • Protein or peptide: Mouse serotonin 5-HT3A receptor in amphipols A8-35
KeywordsPentameric ligand-gated ion channels Serotonin receptor Amphipols / MEMBRANE PROTEIN
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 / excitatory extracellular ligand-gated monoatomic ion channel activity / serotonin binding / inorganic cation transmembrane transport / acetylcholine-gated monoatomic cation-selective channel activity / cleavage furrow / transmembrane transporter complex ...Neurotransmitter receptors and postsynaptic signal transmission / serotonin-gated monoatomic cation channel activity / serotonin-activated cation-selective channel complex / serotonin receptor signaling pathway / excitatory extracellular ligand-gated monoatomic ion channel activity / serotonin binding / inorganic cation transmembrane transport / acetylcholine-gated monoatomic cation-selective channel activity / cleavage furrow / transmembrane transporter complex / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / presynaptic membrane / postsynaptic membrane / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / identical protein binding / plasma membrane
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: 3.4 Å
AuthorsLopez-Sanchez U / Nury H / Michon B / Zoonens M
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0011-01 France
CitationJournal: Biophys J / Year: 2023
Title: Role of surfactants in electron cryo-microscopy film preparation.
Authors: Baptiste Michon / Uriel López-Sánchez / Jéril Degrouard / Hugues Nury / Amélie Leforestier / Emmanuelle Rio / Anniina Salonen / Manuela Zoonens /
Abstract: Single-particle electron cryo-microscopy (cryo-EM) has become an effective and straightforward approach to determine the structure of membrane proteins. However, obtaining cryo-EM grids of sufficient ...Single-particle electron cryo-microscopy (cryo-EM) has become an effective and straightforward approach to determine the structure of membrane proteins. However, obtaining cryo-EM grids of sufficient quality for high-resolution structural analysis remains a major bottleneck. One of the difficulties arises from the presence of detergents, which often leads to a lack of control of the ice thickness. Amphipathic polymers such as amphipols (APols) are detergent substitutes, which have proven to be valuable tools for cryo-EM studies. In this work, we investigate the physico-chemical behavior of APol- and detergent-containing solutions and show a correlation with the properties of vitreous thin films in cryo-EM grids. This study provides new insight on the potential of APols, allowing a better control of ice thickness while limiting protein adsorption at the air-water interface, as shown with the full-length mouse serotonin 5-HT receptor whose structure has been solved in APol. These findings may speed up the process of grid optimization to obtain high-resolution structures of membrane proteins.
History
DepositionJul 26, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15471.png

Downloads & links

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Map

FileDownload / File: emd_15471.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationm5HT3A receptor in A8-35 amphipols
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 293.12 Å		1.15 Å/pix.
x 256 pix.
= 293.12 Å		1.15 Å/pix.
x 256 pix.
= 293.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.145 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.4075544 - 2.0290089
Average (Standard dev.)0.00013454926 (±0.04410615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 293.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: m5HT3A receptor in A8-35 amphipols half map B

Fileemd_15471_half_map_1.map
Annotationm5HT3A receptor in A8-35 amphipols half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: m5HT3A receptor in A8-35 amphipols half map A

Fileemd_15471_half_map_2.map
Annotationm5HT3A receptor in A8-35 amphipols half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homopentameric complex of 5-HT3A receptor subunits

EntireName: Homopentameric complex of 5-HT3A receptor subunits
Components
  • Complex: Homopentameric complex of 5-HT3A receptor subunits
    • Protein or peptide: Mouse serotonin 5-HT3A receptor in amphipols A8-35

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Supramolecule #1: Homopentameric complex of 5-HT3A receptor subunits

SupramoleculeName: Homopentameric complex of 5-HT3A receptor subunits / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Mouse serotonin 5-HT3A receptor in amphipols A8-35

MacromoleculeName: Mouse serotonin 5-HT3A receptor in amphipols A8-35 / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRLCIPQVLL ALFLSMLTGP GEGSRRRWSH PQFEKGGGSG GGSGGGSWSH PQFEKGGGSG GGSGGGSWSH PQFEKGGGSG GGSGGGSWSH PQFEKENLYF QGSGATQARD TTQPALLRLS DHLLANYKKG VRPVRDWRKP TTVSIDVIMY AILNVDEKNQ VLTTYIWYRQ ...String:
MRLCIPQVLL ALFLSMLTGP GEGSRRRWSH PQFEKGGGSG GGSGGGSWSH PQFEKGGGSG GGSGGGSWSH PQFEKGGGSG GGSGGGSWSH PQFEKENLYF QGSGATQARD TTQPALLRLS DHLLANYKKG VRPVRDWRKP TTVSIDVIMY AILNVDEKNQ VLTTYIWYRQ YWTDEFLQWT PEDFDNVTKL SIPTDSIWVP DILINEFVDV GKSPNIPYVY VHHRGEVQNY KPLQLVTACS LDIYNFPFDV QNCSLTFTSW LHTIQDINIT LWRSPEEVRS DKSIFINQGE WELLEVFPQF KEFSIDISNS YAEMKFYVII RRRPLFYAVS LLLPSIFLMV VDIVGFCLPP DSGERVSFKI TLLLGYSVFL IIVSDTLPAT AIGTPLIGVY FVVCMALLVI SLAETIFIVR LVHKQDLQRP VPDWLRHLVL DRIAWILCLG EQPMAHRPPA TFQANKTDDC SAMGNHCSHV GGPQDLEKTP RGRGSPLPPP REASLAVRGL LQELSSIRHF LEKRDEMREV ARDWLRVGYV LDRLLFRIYL LAVLAYSITL VTLWSIWHSS

UniProtKB: 5-hydroxytryptamine receptor 3A

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35020
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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