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- EMDB-19420: Sub-tomogram averaging results of pentameric 5-HT3A receptor on c... -

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Basic information

Entry
Database: EMDB / ID: EMD-19420
TitleSub-tomogram averaging results of pentameric 5-HT3A receptor on cell-derived vesicles
Map data
Sample
  • Organelle or cellular component: 5-hydroxytryptamine receptor 3A pentamer
    • Protein or peptide: 5-hydroxytryptamine receptor 3A pentamer
Keywords5ht3Ar / pentamer / in-situ subtomogram-averaging / cell-derived vesicles / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 19.6 Å
AuthorsChu X / Kudryashev M
Funding support Germany, China, 5 items
OrganizationGrant numberCountry
Helmholtz Association Germany
German Research Foundation (DFG) Germany
Alexander von Humboldt Foundation Germany
Chinese Academy of Sciences China
Other government
CitationJournal: EMBO J / Year: 2024
Title: Structure of tetrameric forms of the serotonin-gated 5-HT3 receptor ion channel.
Authors: Bianca Introini / Wenqiang Cui / Xiaofeng Chu / Yingyi Zhang / Ana Catarina Alves / Luise Eckhardt-Strelau / Sabrina Golusik / Menno Tol / Horst Vogel / Shuguang Yuan / Mikhail Kudryashev /
Abstract: Multimeric membrane proteins are produced in the endoplasmic reticulum and transported to their target membranes which, for ion channels, is typically the plasma membrane. Despite the availability of ...Multimeric membrane proteins are produced in the endoplasmic reticulum and transported to their target membranes which, for ion channels, is typically the plasma membrane. Despite the availability of many fully assembled channel structures, our understanding of assembly intermediates, multimer assembly mechanisms, and potential functions of non-standard assemblies is limited. We demonstrate that the pentameric ligand-gated serotonin 5-HT3A receptor (5-HT3AR) can assemble to tetrameric forms and report the structures of the tetramers in plasma membranes of cell-derived microvesicles and in membrane memetics using cryo-electron microscopy and tomography. The tetrameric structures have near-symmetric transmembrane domains, and asymmetric extracellular domains, and can bind serotonin molecules. Computer simulations, based on our cryo-EM structures, were used to decipher the assembly pathway of pentameric 5-HT3R and suggest a potential functional role for the tetrameric receptors.
History
DepositionJan 16, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19420.png

Downloads & links

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Map

FileDownload / File: emd_19420.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
5.52 Å/pix.
x 64 pix.
= 353.28 Å		5.52 Å/pix.
x 64 pix.
= 353.28 Å		5.52 Å/pix.
x 64 pix.
= 353.28 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 5.52 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0026
Minimum - Maximum-0.0036370794 - 0.009815683
Average (Standard dev.)0.00020821366 (±0.0006914972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19420_msk_1.map
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Half map: #2

Fileemd_19420_half_map_1.map
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Half map: #1

Fileemd_19420_half_map_2.map
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Sample components

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Entire : 5-hydroxytryptamine receptor 3A pentamer

EntireName: 5-hydroxytryptamine receptor 3A pentamer
Components
  • Organelle or cellular component: 5-hydroxytryptamine receptor 3A pentamer
    • Protein or peptide: 5-hydroxytryptamine receptor 3A pentamer

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Supramolecule #1: 5-hydroxytryptamine receptor 3A pentamer

SupramoleculeName: 5-hydroxytryptamine receptor 3A pentamer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: 5-hydroxytryptamine receptor 3A pentamer

MacromoleculeName: 5-hydroxytryptamine receptor 3A pentamer / type: protein_or_peptide / ID: 1
Details: StrepII-tags, linkers, TEV protease recognition sequence, mouse 5HT3AR (with Ala insertion at position 277 (in the M2-M3 linker) as found in the human receptor)
Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString: MWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKE NLYFQGATQA RDTTQPALLR LSDHLLANYK KGVRPVRDWR KPTTVSIDVI MYAILNVDEK NQVLTTYIWY RQYWTDEFLQ WTPEDFDNVT KLSIPTDSIW ...String:
MWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKE NLYFQGATQA RDTTQPALLR LSDHLLANYK KGVRPVRDWR KPTTVSIDVI MYAILNVDEK NQVLTTYIWY RQYWTDEFLQ WTPEDFDNVT KLSIPTDSIW VPDILINEFV DVGKSPNIPY VYVHHRGEVQ NYKPLQLVTA CSLDIYNFPF DVQNCSLTFT SWLHTIQDIN ITLWRSPEEV RSDKSIFINQ GEWELLEVFP QFKEFSIDIS NSYAEMKFYV IIRRRPLFYA VSLLLPSIFL MVVDIVGFCL PPDSGERVSF KITLLLGYSV FLIIVSDTLP ATAIGTPLIG VYFVVCMALL VISLAETIFI VRLVHKQDLQ RPVPDWLRHL VLDRIAWILC LGEQPMAHRP PATFQANKTD DCSGSDLLPA MGNHCSHVGG PQDLEKTPRG RGSPLPPPRE ASLAVRGLLQ ELSSIRHFLE KRDEMREVAR DWLRVGYVLD RLLFRIYLLA VLAYSITLVT LWSIWHSS

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 4.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 3.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 19.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 3031
ExtractionNumber tomograms: 309 / Number images used: 30623
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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