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Open data
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Basic information
Entry | Database: PDB / ID: 6y59 | ||||||
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Title | 5-HT3A receptor in Salipro (apo, C5 symmetric) | ||||||
![]() | 5-hydroxytryptamine receptor 3A | ||||||
![]() | MEMBRANE PROTEIN / Pentameric ligand-gated ion channel / pLGIC / serotonin 5-HT3A receptor / 5-HT3AR / Salipro | ||||||
Function / homology | ![]() 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 / cleavage furrow / transmembrane transporter complex / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ...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 / 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
![]() | Zhang, Y. / Dijkman, P.M. / Zou, R. / Zandl-Lang, M. / Sanchez, R.M. / Eckhardt-Strelau, L. / Koefeler, H. / Vogel, H. / Yuan, S. / Kudryashev, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Asymmetric opening of the homopentameric 5-HT serotonin receptor in lipid bilayers. Authors: Yingyi Zhang / Patricia M Dijkman / Rongfeng Zou / Martina Zandl-Lang / Ricardo M Sanchez / Luise Eckhardt-Strelau / Harald Köfeler / Horst Vogel / Shuguang Yuan / Mikhail Kudryashev / ![]() ![]() ![]() ![]() Abstract: Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop receptor family are key players in fast signal transduction throughout the nervous system. They have been shown to be modulated by the ...Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop receptor family are key players in fast signal transduction throughout the nervous system. They have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. We report three structures of the Cys-loop 5-HT serotonin receptor (5HTR) reconstituted into saposin-based lipid bilayer discs: a symmetric and an asymmetric apo state, and an asymmetric agonist-bound state. In comparison to previously published 5HTR conformations in detergent, the lipid bilayer stabilises the receptor in a more tightly packed, 'coupled' state, involving a cluster of highly conserved residues. In consequence, the agonist-bound receptor conformation adopts a wide-open pore capable of conducting sodium ions in unbiased molecular dynamics (MD) simulations. Taken together, we provide a structural basis for the modulation of 5HTR by the membrane environment, and a model for asymmetric activation of the receptor. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 655.8 KB | Display | ![]() |
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PDB format | ![]() | 564.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10691MC ![]() 6y5aC ![]() 6y5bC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 15.6 TB Data #1: Lipid-stabilised 5-HT3A serotonin receptor in asymmetric open state [micrographs - multiframe] Data #2: Lipid-stabilised 5-HT3A serotonin receptor in apo state forms (symmetric C5 apo and asymmetric C1 apo) [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 60668.086 Da / Num. of mol.: 5 / Mutation: Insertion A277 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 5-hydroxytryptamine receptor 3A (apo) embedded in saposin lipid disc Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
EM software | Name: RELION / Version: 3 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C5 (5 fold cyclic) |
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 238701 / Symmetry type: POINT |