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- EMDB-3108: Structure of the mouse serotonin receptor 5-HT3 in lipid vesicles -

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Basic information

Entry
Database: EMDB / ID: EMD-3108
TitleStructure of the mouse serotonin receptor 5-HT3 in lipid vesicles
Map dataReconstruction of the mouse 5-HT3 receptor in lipid vesicles by sub-tomogram averaging.
Sample
  • Sample: Mouse serotonin receptor 5-HT3
  • Protein or peptide: 5-hydroxytryptamine receptor5-HT receptor
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)
Methodsubtomogram averaging / cryo EM / negative staining / Resolution: 12.0 Å
AuthorsKudryashev M / Castano-Diez D / Deluz C / Hassaine G / Graf-Meyer A / Vogel H / Stahlberg H
CitationJournal: Structure / Year: 2016
Title: The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles.
Authors: Mikhail Kudryashev / Daniel Castaño-Díez / Cédric Deluz / Gherici Hassaine / Luigino Grasso / Alexandra Graf-Meyer / Horst Vogel / Henning Stahlberg /
Abstract: The function of membrane proteins is best understood if their structure in the lipid membrane is known. Here, we determined the structure of the mouse serotonin 5-HT3 receptor inserted in lipid ...The function of membrane proteins is best understood if their structure in the lipid membrane is known. Here, we determined the structure of the mouse serotonin 5-HT3 receptor inserted in lipid bilayers to a resolution of 12 Å without stabilizing antibodies by cryo electron tomography and subtomogram averaging. The reconstruction reveals protein secondary structure elements in the transmembrane region, the extracellular pore, and the transmembrane channel pathway, showing an overall similarity to the available X-ray model of the truncated 5-HT3 receptor determined in the presence of a stabilizing nanobody. Structural analysis of the 5-HT3 receptor embedded in a lipid bilayer allowed the position of the membrane to be determined. Interactions between the densely packed receptors in lipids were visualized, revealing that the interactions were maintained by the short horizontal helices. In combination with methodological improvements, our approach enables the structural analysis of membrane proteins in response to voltage and ligand gating.
History
DepositionJul 24, 2015-
Header (metadata) releaseAug 19, 2015-
Map releaseJan 13, 2016-
UpdateJan 27, 2016-
Current statusJan 27, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3108.tif

Downloads & links

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Map

FileDownload / File: emd_3108.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the mouse 5-HT3 receptor in lipid vesicles by sub-tomogram averaging.
Voxel sizeX=Y=Z: 1.67 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 1
Minimum - Maximum-2.6561017 - 8.42369843
Average (Standard dev.)0.0 (±0.99999976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 213.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.671.671.67
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z213.760213.760213.760
α/β/γ90.00090.00090.000
start NX/NY/NZ-180-180-179
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-2.6568.4240.000

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Supplemental data

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Segmentation: mask for the final visualization, contains one pentamer

Annotationmask for the final visualization, contains one pentamer
Fileemd_3108_msk_1.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 : Mouse serotonin receptor 5-HT3

EntireName: Mouse serotonin receptor 5-HT3
Components
  • Sample: Mouse serotonin receptor 5-HT3
  • Protein or peptide: 5-hydroxytryptamine receptor5-HT receptor

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Supramolecule #1000: Mouse serotonin receptor 5-HT3

SupramoleculeName: Mouse serotonin receptor 5-HT3 / type: sample / ID: 1000 / Oligomeric state: pentamer / Number unique components: 1
Molecular weightTheoretical: 244 MDa

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Macromolecule #1: 5-hydroxytryptamine receptor

MacromoleculeName: 5-hydroxytryptamine receptor / type: protein_or_peptide / ID: 1 / Name.synonym: 5-HT3 / Details: Protein reconstituted into lipid vesicles. / Number of copies: 5 / Oligomeric state: pentamer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse / Location in cell: Plasma membrane
Molecular weightTheoretical: 244 MDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: T-REx-293 cells / Recombinant plasmid: pcDNA5/TO
SequenceUniProtKB: 5-hydroxytryptamine receptor 3A

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE / Details: Cryo-preparation
GridDetails: Holey carbon grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 90 K / Instrument: LEICA EM GP / Method: Blot for 2 second before plunding

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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 / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Alignment procedureLegacy - Astigmatism: corrected at high magnification
Detailstomograms acquired without the energy filtration
DateDec 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 46 / Average electron dose: 41 e/Å2 / Details: 46 tomograms were selected for processing
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: ctfplotter
Final 3D classificationNumber classes: 20
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Software - Name: IMOD, Dynamo / Number subtomograms used: 16000
DetailsParticles were automatically picked from the surface of the vesicles in CTF-corrected cryo-electron tomograms. After a rough alignment deep classification into 20 classes was performed including 4 neighbouring pentamers in the alignment mask. Finally the central pentamers from each class were cropped, aligned and averaged resulting in a final structure.

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