+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10692 | |||||||||
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Title | Serotonin-bound 5-HT3A receptor in Salipro | |||||||||
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Sample |
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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 / 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 | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Zhang Y / Dijkman PM / Zou R / Zandl-Lang M / Sanchez RM / Eckhardt-Strelau L / Koefeler H / Vogel H / Yuan S / Kudryashev M | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10692.map.gz | 8.9 MB | EMDB map data format | |
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Header (meta data) | emd-10692-v30.xml emd-10692.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10692_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_10692.png | 82.5 KB | ||
Masks | emd_10692_msk_1.map | 125 MB | Mask map | |
Others | emd_10692_additional_1.map.gz emd_10692_half_map_1.map.gz emd_10692_half_map_2.map.gz | 98.3 MB 99.1 MB 99.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10692 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10692 | HTTPS FTP |
-Validation report
Summary document | emd_10692_validation.pdf.gz | 376.9 KB | Display | EMDB validaton report |
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Full document | emd_10692_full_validation.pdf.gz | 376 KB | Display | |
Data in XML | emd_10692_validation.xml.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10692 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10692 | HTTPS FTP |
-Related structure data
Related structure data | 6y5aMC 6y59C 6y5bC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10381 (Title: Lipid-stabilised asymmetric open state of the 5-HT3A serotonin receptor 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]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10692.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10692_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_10692_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_10692_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_10692_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : 5-hydroxytryptamine receptor 3A bound to 5-HT embedded in saposin...
Entire | Name: 5-hydroxytryptamine receptor 3A bound to 5-HT embedded in saposin lipid disc |
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Components |
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-Supramolecule #1: 5-hydroxytryptamine receptor 3A bound to 5-HT embedded in saposin...
Supramolecule | Name: 5-hydroxytryptamine receptor 3A bound to 5-HT embedded in saposin lipid disc type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: 5-hydroxytryptamine receptor 3A
Macromolecule | Name: 5-hydroxytryptamine receptor 3A / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 60.668086 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: SEROTONIN
Macromolecule | Name: SEROTONIN / type: ligand / ID: 2 / Number of copies: 5 / Formula: SRO |
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Molecular weight | Theoretical: 176.215 Da |
Chemical component information | ChemComp-SRO: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |