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Yorodumi- EMDB-26160: Structure of human serotonin transporter bound to small molecule ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26160 | |||||||||
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Title | Structure of human serotonin transporter bound to small molecule '8090 in lipid nanodisc and NaCl | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Neurotransmitter transporter / small molecule / membrane protein / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / serotonergic synapse / positive regulation of serotonin secretion / cocaine binding / serotonin:sodium:chloride symporter activity / negative regulation of synaptic transmission, dopaminergic / sperm ejaculation / enteric nervous system development ...negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / serotonergic synapse / positive regulation of serotonin secretion / cocaine binding / serotonin:sodium:chloride symporter activity / negative regulation of synaptic transmission, dopaminergic / sperm ejaculation / enteric nervous system development / serotonin uptake / cellular response to cGMP / negative regulation of organ growth / sodium ion binding / neurotransmitter transmembrane transporter activity / conditioned place preference / monoamine transmembrane transporter activity / monoamine transport / serotonin binding / vasoconstriction / brain morphogenesis / neurotransmitter transport / antiporter activity / 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 / response to nutrient / cellular response to retinoic acid / circadian rhythm / response to toxic substance / memory / platelet aggregation / actin filament binding / integrin binding / response to estradiol / presynaptic membrane / postsynaptic membrane / endosome membrane / response to hypoxia / 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: 3.0 Å | |||||||||
Authors | Singh I / Seth A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2023 Title: Structure-based discovery of conformationally selective inhibitors of the serotonin transporter. Authors: Isha Singh / Anubha Seth / Christian B Billesbølle / Joao Braz / Ramona M Rodriguiz / Kasturi Roy / Bethlehem Bekele / Veronica Craik / Xi-Ping Huang / Danila Boytsov / Vladimir M Pogorelov ...Authors: Isha Singh / Anubha Seth / Christian B Billesbølle / Joao Braz / Ramona M Rodriguiz / Kasturi Roy / Bethlehem Bekele / Veronica Craik / Xi-Ping Huang / Danila Boytsov / Vladimir M Pogorelov / Parnian Lak / Henry O'Donnell / Walter Sandtner / John J Irwin / Bryan L Roth / Allan I Basbaum / William C Wetsel / Aashish Manglik / Brian K Shoichet / Gary Rudnick / Abstract: The serotonin transporter (SERT) removes synaptic serotonin and is the target of anti-depressant drugs. SERT adopts three conformations: outward-open, occluded, and inward-open. All known inhibitors ...The serotonin transporter (SERT) removes synaptic serotonin and is the target of anti-depressant drugs. SERT adopts three conformations: outward-open, occluded, and inward-open. All known inhibitors target the outward-open state except ibogaine, which has unusual anti-depressant and substance-withdrawal effects, and stabilizes the inward-open conformation. Unfortunately, ibogaine's promiscuity and cardiotoxicity limit the understanding of inward-open state ligands. We docked over 200 million small molecules against the inward-open state of the SERT. Thirty-six top-ranking compounds were synthesized, and thirteen inhibited; further structure-based optimization led to the selection of two potent (low nanomolar) inhibitors. These stabilized an outward-closed state of the SERT with little activity against common off-targets. A cryo-EM structure of one of these bound to the SERT confirmed the predicted geometry. In mouse behavioral assays, both compounds had anxiolytic- and anti-depressant-like activity, with potencies up to 200-fold better than fluoxetine (Prozac), and one substantially reversed morphine withdrawal effects. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26160.map.gz | 89.5 MB | EMDB map data format | |
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Header (meta data) | emd-26160-v30.xml emd-26160.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_26160.png | 79 KB | ||
Filedesc metadata | emd-26160.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26160 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26160 | HTTPS FTP |
-Validation report
Summary document | emd_26160_validation.pdf.gz | 465 KB | Display | EMDB validaton report |
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Full document | emd_26160_full_validation.pdf.gz | 464.6 KB | Display | |
Data in XML | emd_26160_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_26160_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26160 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26160 | HTTPS FTP |
-Related structure data
Related structure data | 7txtMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26160.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.81 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Human serotonin transporter in complex with Fab15B8 bound to '809...
Entire | Name: Human serotonin transporter in complex with Fab15B8 bound to '8090 in NaCl |
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Components |
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-Supramolecule #1: Human serotonin transporter in complex with Fab15B8 bound to '809...
Supramolecule | Name: Human serotonin transporter in complex with Fab15B8 bound to '8090 in NaCl type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: Sodium-dependent serotonin transporter
Supramolecule | Name: Sodium-dependent serotonin transporter / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Fab15B8 heavy chain
Supramolecule | Name: Fab15B8 heavy chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #4: Fab15B8 light chain
Supramolecule | Name: Fab15B8 light chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: 15B8 Fab heavy chain
Macromolecule | Name: 15B8 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 13.166742 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQQSGPE LVKLGASVRI SCKASGYRFS YSWMNWVKQR PGKGLEWIGR IYPGDGDTKY SGKFKGKATL TADKSSSTVY MQLSSLTSE DSAVYFCARS AYGSEGFAMD YWGQGTSVTV S |
-Macromolecule #2: 15B8 Fab light chain
Macromolecule | Name: 15B8 Fab light 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: 11.905246 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIVLTQSPAS LAVSLGQRAT ISCRASESVD NYGISFLNWF QQKPGQPPKL LIYAASNQGS GVPARFSGSG SGTYFSLNIH PMEEDDTAV YFCQQTKGVS WTFGGGTKVE IK |
-Macromolecule #3: Sodium-dependent serotonin transporter
Macromolecule | Name: Sodium-dependent serotonin transporter / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 61.062129 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GERETWGKKV DFLLSVIGYA VDLGNVWRFP YICYQNGGGA FLLPYTIMAI FGGIPLFYME LALGQYHRNG CISIWRKICP IFKGIGYAI CIIAFYIASY YNTIMAWALY YLISSFTDQL PWTSCKNSWN TGNCTNYFSE DNITWTLHST SPAEEFYTRH V LQIHRSKG ...String: GERETWGKKV DFLLSVIGYA VDLGNVWRFP YICYQNGGGA FLLPYTIMAI FGGIPLFYME LALGQYHRNG CISIWRKICP IFKGIGYAI CIIAFYIASY YNTIMAWALY YLISSFTDQL PWTSCKNSWN TGNCTNYFSE DNITWTLHST SPAEEFYTRH V LQIHRSKG LQDLGGISWQ LALCIMLIFT VIYFSIWKGV KTSGKVVWVT ATFPYIILSV LLVRGATLPG AWRGVLFYLK PN WQKLLET GVWIDAAAQI FFSLGPGFGV LLAFASYNKF NNNCYQDALV TSVVNCMTSF VSGFVIFTVL GYMAEMRNED VSE VAKDAG PSLLFITYAE AIANMPASTF FAIIFFLMLI TLGLDSTFAG LEGVITAVLD EFPHVWAKRR ERFVLAVVIT CFFG SLVTL TFGGAYVVKL LEEYATGPAV LTVALIEAVA VSWFYGITQF CRDVKEMLGF SPGWFWRICW VAISPLFLLF IICSF LMSP PQLRLFQYNY PYWSIILGYC IGTSSFICIP TYIAYRLIIT PGTFKERIIK SITPETP UniProtKB: Sodium-dependent serotonin transporter |
-Macromolecule #4: 1-[4-(4-fluorophenyl)-1,3-thiazol-2-yl]piperazine
Macromolecule | Name: 1-[4-(4-fluorophenyl)-1,3-thiazol-2-yl]piperazine / type: ligand / ID: 4 / Number of copies: 1 / Formula: KWC |
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Molecular weight | Theoretical: 263.334 Da |
Chemical component information | ChemComp-KWC: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k 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 / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Ab initio reconstruction |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 187696 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.2.0) |