6DZW

Cryo-EM structure of the ts2-inactive human serotonin transporter in complex with paroxetine and 15B8 Fab and 8B6 ScFv


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport.

Coleman, J.A.Yang, D.Zhao, Z.Wen, P.C.Yoshioka, C.Tajkhorshid, E.Gouaux, E.

(2019) Nature 569: 141-145

  • DOI: 10.1038/s41586-019-1135-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The serotonin transporter (SERT) regulates neurotransmitter homeostasis through the sodium- and chloride-dependent recycling of serotonin into presynaptic neurons <sup>1-3 </sup>. Major depression and anxiety disorders are treated using selective ser ...

    The serotonin transporter (SERT) regulates neurotransmitter homeostasis through the sodium- and chloride-dependent recycling of serotonin into presynaptic neurons 1-3 . Major depression and anxiety disorders are treated using selective serotonin reuptake inhibitors-small molecules that competitively block substrate binding and thereby prolong neurotransmitter action 2,4 . 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 2,3 , and genetic variants of NSSs are associated with several neuropsychiatric disorders including attention deficit hyperactivity disorder, autism and bipolar disorder 2,5 . 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 1,6-12 . 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 13,14 . Notably, ibogaine is a non-competitive inhibitor of transport but displays competitive binding towards selective serotonin reuptake inhibitors 15,16 . 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.


    Organizational Affiliation

    Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR, USA. gouauxe@ohsu.edu.,Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Vollum Institute, Oregon Health & Science University, Portland, OR, USA. gouauxe@ohsu.edu.,Vollum Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium-dependent serotonin transporter
A
537Homo sapiensMutation(s): 0 
Gene Names: SLC6A4 (HTT, SERT)
Find proteins for P31645 (Homo sapiens)
Go to Gene View: SLC6A4
Go to UniProtKB:  P31645
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
8B6 antibody single chain
V
240N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
15B8 antibody heavy chain
H
118N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
15B8 antibody light chain
L
110N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8PR
Query on 8PR

Download SDF File 
Download CCD File 
A
Paroxetine
(3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine
C19 H20 F N O3
AHOUBRCZNHFOSL-YOEHRIQHSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
V
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--
National Institutes of Health/National Institute of Mental HealthUnited States5R37MH070039

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-06-05
    Type: Data collection, Database references