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Yorodumi- EMDB-8943: Cryo-EM Structure of the wild-type human serotonin transporter in... -
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-Basic information
Entry | Database: EMDB / ID: EMD-8943 | |||||||||
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Title | Cryo-EM Structure of the wild-type human serotonin transporter in complex with ibogaine and 15B8 Fab in the inward conformation | |||||||||
Map data | Wild-type SERT bound to Fab and in complex with ibogaine in the occluded and inward conformations | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / serotonergic synapse / Serotonin clearance from the synaptic cleft / positive regulation of serotonin secretion / cocaine binding / negative regulation of synaptic transmission, dopaminergic / sperm ejaculation / serotonin:sodium:chloride symporter activity / sodium ion binding ...negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / serotonergic synapse / Serotonin clearance from the synaptic cleft / positive regulation of serotonin secretion / cocaine binding / negative regulation of synaptic transmission, dopaminergic / sperm ejaculation / serotonin:sodium:chloride symporter activity / sodium ion binding / cellular response to cGMP / enteric nervous system development / negative regulation of organ growth / serotonin uptake / neurotransmitter transmembrane transporter activity / serotonin binding / monoamine transmembrane transporter activity / monoamine transport / conditioned place preference / vasoconstriction / brain morphogenesis / antiporter activity / neurotransmitter transport / syntaxin-1 binding / amino acid transport / nitric-oxide synthase binding / membrane depolarization / behavioral response to cocaine / social behavior / negative regulation of neuron differentiation / sodium ion transmembrane transport / endomembrane system / monoatomic cation channel activity / positive regulation of cell cycle / cellular response to retinoic acid / response to nutrient / platelet aggregation / memory / response to toxic substance / circadian rhythm / actin filament binding / integrin binding / response to estradiol / presynaptic membrane / postsynaptic membrane / response to hypoxia / endosome membrane / neuron projection / response to xenobiotic stimulus / membrane raft / focal adhesion / synapse / positive regulation of gene expression / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 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_8943.map.gz | 194.3 MB | EMDB map data format | |
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Header (meta data) | emd-8943-v30.xml emd-8943.xml | 37.2 KB 37.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8943_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_8943.png | 672.7 KB | ||
Masks | emd_8943_msk_1.map emd_8943_msk_2.map | 209.3 MB 209.3 MB | Mask map | |
Others | emd_8943_additional_1.map.gz emd_8943_additional_2.map.gz emd_8943_additional_3.map.gz emd_8943_additional_4.map.gz emd_8943_additional_5.map.gz emd_8943_additional_6.map.gz emd_8943_additional_7.map.gz emd_8943_additional_8.map.gz emd_8943_additional_9.map.gz emd_8943_half_map_1.map.gz emd_8943_half_map_2.map.gz | 116.1 MB 115.6 MB 11.5 MB 11.5 MB 115.8 MB 115.7 MB 115.1 MB 194.3 MB 191.2 MB 23.4 MB 23.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8943 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8943 | HTTPS FTP |
-Validation report
Summary document | emd_8943_validation.pdf.gz | 761 KB | Display | EMDB validaton report |
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Full document | emd_8943_full_validation.pdf.gz | 760.5 KB | Display | |
Data in XML | emd_8943_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_8943_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8943 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8943 | HTTPS FTP |
-Related structure data
Related structure data | 6dzzMC 0437C 8940C 8941C 8942C 6d9gC 6dzvC 6dzwC 6dzyC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8943.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Wild-type SERT bound to Fab and in complex with ibogaine in the occluded and inward conformations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.823 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Mask #2
+Additional map: Unsharpened map, data set 2
+Additional map: Unsharpened map, data set 1
+Additional map: half map 2, data set 2
+Additional map: half map 1, data set 2
+Additional map: Inward class, data set 1
+Additional map: Occluded class, data set 1
+Additional map: Unsharpened, aligned and averaged map from data set 1 and 2
+Additional map: inward class, low resolution
+Additional map: inward class, unsharpened map
+Half map: Half map 2, data set 1
+Half map: Half map 1, data set 1
-Sample components
-Entire : Human serotonin transporter in complex with Fab bound to ibogaine
Entire | Name: Human serotonin transporter in complex with Fab bound to ibogaine |
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Components |
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-Supramolecule #1: Human serotonin transporter in complex with Fab bound to ibogaine
Supramolecule | Name: Human serotonin transporter in complex with Fab bound to ibogaine type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: serotonin transporter
Supramolecule | Name: serotonin transporter / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: 15B8 Fab
Supramolecule | Name: 15B8 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Sodium-dependent serotonin transporter
Macromolecule | Name: Sodium-dependent serotonin transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 61.005074 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ERETWGKKVD FLLSVIGYAV DLGNVWRFPY ICYQNGGGAF LLPYTIMAIF GGIPLFYMEL ALGQYHRNGC ISIWRKICPI FKGIGYAIC IIAFYIASYY NTIMAWALYY LISSFTDQLP WTSCKNSWNT GNCTNYFSED NITWTLHSTS PAEEFYTRHV L QIHRSKGL ...String: ERETWGKKVD FLLSVIGYAV DLGNVWRFPY ICYQNGGGAF LLPYTIMAIF GGIPLFYMEL ALGQYHRNGC ISIWRKICPI FKGIGYAIC IIAFYIASYY NTIMAWALYY LISSFTDQLP WTSCKNSWNT GNCTNYFSED NITWTLHSTS PAEEFYTRHV L QIHRSKGL QDLGGISWQL ALCIMLIFTV IYFSIWKGVK TSGKVVWVTA TFPYIILSVL LVRGATLPGA WRGVLFYLKP NW QKLLETG VWIDAAAQIF FSLGPGFGVL LAFASYNKFN NNCYQDALVT SVVNCMTSFV SGFVIFTVLG YMAEMRNEDV SEV AKDAGP SLLFITYAEA IANMPASTFF AIIFFLMLIT LGLDSTFAGL EGVITAVLDE FPHVWAKRRE RFVLAVVITC FFGS LVTLT FGGAYVVKLL EEYATGPAVL TVALIEAVAV SWFYGITQFC RDVKEMLGFS PGWFWRICWV AISPLFLLFI ICSFL MSPP QLRLFQYNYP YWSIILGYCI GTSSFICIPT YIAYRLIITP GTFKERIIKS ITPETP |
-Macromolecule #2: 15B8 antibody heavy chain
Macromolecule | Name: 15B8 antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 12.980533 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: QVQLQQSGPE LVKLGASVRI SCKASGYRFS YSWMNWVKQR PGKGLEWIGR IYPGDGDTKY SGKFKGKATL TADKSSSTVY MQLSSLTSE DSAVYFCARS AYGSEGFAMD YWGQGTSVT |
-Macromolecule #3: 15B8 antibody light chain
Macromolecule | Name: 15B8 antibody light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 11.776065 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: DIVLTQSPAS LAVSLGQRAT ISCRASESVD NYGISFLNWF QQKPGQPPKL LIYAASNQGS GVPARFSGSG SGTYFSLNIH PMEEDDTAV YFCQQTKGVS WTFGGGTKVE I |
-Macromolecule #5: (5beta)-12-methoxyibogamine
Macromolecule | Name: (5beta)-12-methoxyibogamine / type: ligand / ID: 5 / Number of copies: 1 / Formula: HJM |
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Molecular weight | Theoretical: 310.433 Da |
Chemical component information | ChemComp-HJM: |
-Macromolecule #6: DODECYL-BETA-D-MALTOSIDE
Macromolecule | Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 6 / Number of copies: 1 / Formula: LMT |
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Molecular weight | Theoretical: 510.615 Da |
Chemical component information | ChemComp-LMT: |
-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 TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 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 |