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Yorodumi- EMDB-0437: Cryo-EM structure of the wild-type human serotonin transporter in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0437 | |||||||||
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Title | Cryo-EM structure of the wild-type human serotonin transporter in complex with 15B8 Fab bound to noribogaine | |||||||||
Map data | wild-type human serotonin transporter in complex with 15B8 Fab bound to noribogaine, sharpened map | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Yang D / Coleman JA / Gouaux E | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2019 Title: Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport. Authors: Jonathan A Coleman / Dongxue Yang / Zhiyu Zhao / Po-Chao Wen / Craig Yoshioka / Emad Tajkhorshid / Eric Gouaux / Abstract: The serotonin transporter (SERT) regulates neurotransmitter homeostasis through the sodium- and chloride-dependent recycling of serotonin into presynaptic neurons. Major depression and anxiety ...The serotonin transporter (SERT) regulates neurotransmitter homeostasis through the sodium- and chloride-dependent recycling of serotonin into presynaptic neurons. Major depression and anxiety disorders are treated using selective serotonin reuptake inhibitors-small molecules that competitively block substrate binding and thereby prolong neurotransmitter action. The dopamine and noradrenaline transporters, together with SERT, are members of the neurotransmitter sodium symporter (NSS) family. The transport activities of NSSs can be inhibited or modulated by cocaine and amphetamines, and genetic variants of NSSs are associated with several neuropsychiatric disorders including attention deficit hyperactivity disorder, autism and bipolar disorder. Studies of bacterial NSS homologues-including LeuT-have shown how their transmembrane helices (TMs) undergo conformational changes during the transport cycle, exposing a central binding site to either side of the membrane. However, the conformational changes associated with transport in NSSs remain unknown. To elucidate structure-based mechanisms for transport in SERT we investigated its complexes with ibogaine, a hallucinogenic natural product with psychoactive and anti-addictive properties. Notably, ibogaine is a non-competitive inhibitor of transport but displays competitive binding towards selective serotonin reuptake inhibitors. Here we report cryo-electron microscopy structures of SERT-ibogaine complexes captured in outward-open, occluded and inward-open conformations. Ibogaine binds to the central binding site, and closure of the extracellular gate largely involves movements of TMs 1b and 6a. Opening of the intracellular gate involves a hinge-like movement of TM1a and the partial unwinding of TM5, which together create a permeation pathway that enables substrate and ion diffusion to the cytoplasm. These structures define the structural rearrangements that occur from the outward-open to inward-open conformations, and provide insight into the mechanism of neurotransmitter transport and ibogaine inhibition. | |||||||||
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_0437.map.gz | 116.1 MB | EMDB map data format | |
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Header (meta data) | emd-0437-v30.xml emd-0437.xml | 8.3 KB 8.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0437_fsc.xml | 12.2 KB | Display | FSC data file |
Images | emd_0437.png | 88.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0437 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0437 | HTTPS FTP |
-Related structure data
Related structure data | 8940C 8941C 8942C 8943C 6d9gC 6dzvC 6dzwC 6dzyC 6dzzC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0437.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | wild-type human serotonin transporter in complex with 15B8 Fab bound to noribogaine, sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.91 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human serotonin transporter in complex with Fab bound to noribogaine
Entire | Name: Human serotonin transporter in complex with Fab bound to noribogaine |
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Components |
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-Supramolecule #1: Human serotonin transporter in complex with Fab bound to noribogaine
Supramolecule | Name: Human serotonin transporter in complex with Fab bound to noribogaine type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |