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- EMDB-16387: Tetrameric 5-HT3A receptor in Salipro (holo, asymmetric) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-16387
TitleTetrameric 5-HT3A receptor in Salipro (holo, asymmetric)
Map dataunfiltered EM map
Sample
  • Complex: Tetrameric 5-HT3aR receptor in Salipro (holo, asymmetric)
    • Protein or peptide: 5-hydroxytryptamine receptor 3A
  • Ligand: SEROTONIN
Keywords5-HT3R / Serotonin / receptor / tetramer / ion channel MEMBRANE PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / serotonin-gated cation-selective signaling pathway / serotonin-activated cation-selective channel complex / serotonin-gated monoatomic cation channel activity / serotonin receptor signaling pathway / serotonin binding / : / cleavage furrow / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / postsynaptic membrane / 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 ...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: 3.6 Å
AuthorsIntroini B / Kudryashev M
Funding support Germany, 1 items
OrganizationGrant numberCountry
Alexander von Humboldt FoundationSofja Kovalevskaja Award to MK Germany
CitationJournal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionDec 21, 2022-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16387.png

Downloads & links

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Map

FileDownload / File: emd_16387.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunfiltered EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 330 pix.
= 276.21 Å		0.84 Å/pix.
x 330 pix.
= 276.21 Å		0.84 Å/pix.
x 330 pix.
= 276.21 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.38659918 - 0.9309419
Average (Standard dev.)-0.00028077964 (±0.027866716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 276.21 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16387_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: filtered EM map used for model generation and fitting

Fileemd_16387_additional_1.map
Annotationfiltered EM map used for model generation and fitting
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map A

Fileemd_16387_half_map_1.map
Annotationunfiltered half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map B

Fileemd_16387_half_map_2.map
Annotationunfiltered half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric 5-HT3aR receptor in Salipro (holo, asymmetric)

EntireName: Tetrameric 5-HT3aR receptor in Salipro (holo, asymmetric)
Components
  • Complex: Tetrameric 5-HT3aR receptor in Salipro (holo, asymmetric)
    • Protein or peptide: 5-hydroxytryptamine receptor 3A
  • Ligand: SEROTONIN

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Supramolecule #1: Tetrameric 5-HT3aR receptor in Salipro (holo, asymmetric)

SupramoleculeName: Tetrameric 5-HT3aR receptor in Salipro (holo, asymmetric)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: 5-hydroxytryptamine receptor 3A

MacromoleculeName: 5-hydroxytryptamine receptor 3A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 60.668086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKE NLYFQGATQA RDTTQPALL RLSDHLLANY KKGVRPVRDW RKPTTVSIDV IMYAILNVDE KNQVLTTYIW YRQYWTDEFL QWTPEDFDNV T KLSIPTDS ...String:
MWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKE NLYFQGATQA RDTTQPALL RLSDHLLANY KKGVRPVRDW RKPTTVSIDV IMYAILNVDE KNQVLTTYIW YRQYWTDEFL QWTPEDFDNV T KLSIPTDS IWVPDILINE FVDVGKSPNI PYVYVHHRGE VQNYKPLQLV TACSLDIYNF PFDVQNCSLT FTSWLHTIQD IN ITLWRSP EEVRSDKSIF INQGEWELLE VFPQFKEFSI DISNSYAEMK FYVIIRRRPL FYAVSLLLPS IFLMVVDIVG FCL PPDSGE RVSFKITLLL GYSVFLIIVS DTLPATAIGT PLIGVYFVVC MALLVISLAE TIFIVRLVHK QDLQRPVPDW LRHL VLDRI AWILCLGEQP MAHRPPATFQ ANKTDDCSGS DLLPAMGNHC SHVGGPQDLE KTPRGRGSPL PPPREASLAV RGLLQ ELSS IRHFLEKRDE MREVARDWLR VGYVLDRLLF RIYLLAVLAY SITLVTLWSI WHSS

UniProtKB: 5-hydroxytryptamine receptor 3A

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Macromolecule #2: SEROTONIN

MacromoleculeName: SEROTONIN / type: ligand / ID: 2 / Number of copies: 2 / Formula: SRO
Molecular weightTheoretical: 176.215 Da
Chemical component information

ChemComp-SRO:
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: 7.6
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm
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:

6y5a


Details: Pentameric 5-HT3A receptor in Salipro (holo, asymmetric)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 338651
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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