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- PDB-9vws: Cryo-EM structure of human serotonin transporter in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9vws
TitleCryo-EM structure of human serotonin transporter in complex with tesofensine
ComponentsSodium-dependent serotonin transporter
KeywordsMEMBRANE PROTEIN / Cryo-EM structure of human serotonin transporter in complex with tesofensine
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 / negative regulation of organ growth / negative regulation of synaptic transmission, dopaminergic / serotonin:sodium:chloride symporter activity / cellular response to cGMP ...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 / negative regulation of organ growth / negative regulation of synaptic transmission, dopaminergic / serotonin:sodium:chloride symporter activity / cellular response to cGMP / sodium ion binding / enteric nervous system development / serotonin uptake / neurotransmitter transmembrane transporter activity / vasoconstriction / brain morphogenesis / monoamine transmembrane transporter activity / : / serotonin binding / antiporter activity / negative regulation of neuron differentiation / syntaxin-1 binding / male mating behavior / nitric-oxide synthase binding / neurotransmitter transport / amino acid transport / membrane depolarization / conditioned place preference / cellular response to retinoic acid / monoatomic cation channel activity / behavioral response to cocaine / response to nutrient / positive regulation of cell cycle / endomembrane system / sodium ion transmembrane transport / circadian rhythm / memory / platelet aggregation / integrin binding / response to toxic substance / actin filament binding / response to estradiol / presynaptic membrane / response to hypoxia / postsynaptic membrane / endosome membrane / neuron projection / response to xenobiotic stimulus / membrane raft / focal adhesion / positive regulation of gene expression / synapse / 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
: / CHOLESTEROL HEMISUCCINATE / Sodium-dependent serotonin transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhao, Y. / Li, Y. / Meng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Cryo-EM structure of human serotonin transporter in complex with tesofensine
Authors: Zhao, Y. / Li, Y. / Meng, Y.
History
DepositionJul 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium-dependent serotonin transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2686
Polymers70,3711
Non-polymers8965
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 70371.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A4, HTT, SERT / Production host: Homo sapiens (human) / References: UniProt: P31645
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1EA1 / (1~{R},2~{R},3~{S},5~{S})-3-(3,4-dichlorophenyl)-2-(ethoxymethyl)-8-methyl-8-azabicyclo[3.2.1]octane / Tesofensine


Mass: 328.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23Cl2NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
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: Cryo-EM structure of human serotonin transporter in complex with tesofensine
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.7.0particle selection
2PHENIX1.19_4092model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174344 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024494
ELECTRON MICROSCOPYf_angle_d0.4786136
ELECTRON MICROSCOPYf_dihedral_angle_d4.749609
ELECTRON MICROSCOPYf_chiral_restr0.038693
ELECTRON MICROSCOPYf_plane_restr0.004739

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