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- PDB-9hco: Outward-open structure of human serotonin transporter bound to vi... -

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Basic information

Entry
Database: PDB / ID: 9hco
TitleOutward-open structure of human serotonin transporter bound to vilazodone
Components
  • 15B8 Fab heavy chain
  • 15B8 Fab light chain
  • Sodium-dependent serotonin transporter
KeywordsMEMBRANE PROTEIN / Monoamine transporter / LeuT fold / antidepressant binding / Inhibitor complex
Function / homology
Function and homology information


negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / positive regulation of serotonin secretion / serotonergic synapse / negative regulation of synaptic transmission, dopaminergic / cocaine binding / serotonin:sodium:chloride symporter activity / cellular response to cGMP / enteric nervous system development ...negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / positive regulation of serotonin secretion / serotonergic synapse / negative regulation of synaptic transmission, dopaminergic / cocaine binding / serotonin:sodium:chloride symporter activity / cellular response to cGMP / enteric nervous system development / negative regulation of organ growth / sodium ion binding / neurotransmitter transmembrane transporter activity / serotonin uptake / vasoconstriction / monoamine transmembrane transporter activity / monoamine transport / serotonin binding / brain morphogenesis / antiporter activity / syntaxin-1 binding / male mating behavior / negative regulation of neuron differentiation / neurotransmitter transport / nitric-oxide synthase binding / amino acid transport / conditioned place preference / membrane depolarization / monoatomic cation channel activity / behavioral response to cocaine / positive regulation of cell cycle / cellular response to retinoic acid / response to nutrient / endomembrane system / sodium ion transmembrane transport / circadian rhythm / response to toxic substance / platelet aggregation / memory / integrin binding / actin filament binding / response to estradiol / presynaptic membrane / postsynaptic membrane / response to hypoxia / neuron projection / endosome membrane / membrane raft / response to xenobiotic stimulus / focal adhesion / synapse / positive regulation of gene expression / identical protein binding / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, serotonin, N-terminal / Serotonin (5-HT) neurotransmitter transporter, N-terminus / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
Chem-YG7 / Sodium-dependent serotonin transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsKalenderoglou, I.E. / Tillmann, P. / Loland, C.J.
Funding support Denmark, European Union, United States, 7items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF22OC0079091 Denmark
Independent Research Fund Denmark - Medical Sciences1030-00036B Denmark
H2020 Marie Curie Actions of the European Commission860954European Union
The Carlsberg Foundation1030-00036B Denmark
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)Z1A DA000389 United States
Novo Nordisk FoundationNNF17SA0024386 Denmark
Novo Nordisk FoundationNNF22OC0075808 Denmark
CitationJournal: To Be Published
Title: Structural basis of serotonin reuptake inhibition by a dual mode orthosteric/allosteric antidepressant
Authors: Kalenderoglou, I.E. / Nygaard, A. / Vogt, C.D. / Turaev, A. / Pape, T. / Adams, N. / Newman, A.H. / Loland, C.J.
History
DepositionNov 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium-dependent serotonin transporter
H: 15B8 Fab heavy chain
L: 15B8 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7157
Polymers124,1923
Non-polymers5234
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sodium-dependent serotonin transporter / SERT / 5HT transporter / 5HTT / Solute carrier family 6 member 4


Mass: 76116.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: human SERT full length with GGS linker, thromvin site, GGS linker, twinII site, GGS linker and His12-tag
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A4, HTT, SERT / Plasmid: pFastBac
Details (production host): Baculovirus-derived vector with SLC6A4 gene insert
Cell line (production host): Expi293 / Production host: Homo sapiens (human) / Strain (production host): HEK293 / References: UniProt: P31645

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Antibody , 2 types, 2 molecules HL

#2: Antibody 15B8 Fab heavy chain


Mass: 24516.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Murine monoclonal antibody (15B8) specific for the human serotonin transporter (SERT)
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pFastBac Dual
Details (production host): Baculovirus expression vector used in BacMam system for protein expression in Sf9 cells.
Cell (production host): Sf9 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody 15B8 Fab light chain


Mass: 23558.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Murine monoclonal antibody (15B8) specific for the human serotonin transporter (SERT)
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pFastBac Dual
Details (production host): Baculovirus expression vector used in BacMam system for protein expression in Sf9 cells.
Cell (production host): Sf9 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)

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Non-polymers , 4 types, 16 molecules

#4: Chemical ChemComp-YG7 / 5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide


Mass: 441.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of the Serotonin Transporter with the antidepressant vilazodone
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293 / Cell: Expi293 / Plasmid: pFastBac
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 20000 nm / Nominal defocus min: 6000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
3EPU3.2image acquisitionIMAGE ACQUISITION
4cryoSPARC3.3.2 - 4.4.1image acquisitionPARTICLE SELECTION AND 3D RECONSTRUCTION
5Coot0.9.8.6image acquisitionREAL SPACE REFINEMENT
6UCSF ChimeraX1.8image acquisitionSTRUCTURE ALIGNMENT
7PHENIX1.21image acquisitionREAL SPACE REFINEMENT - VALIDATION - LIGAND PARAMETERIZATION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239223 / Symmetry type: POINT

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