6AWP

X-ray structure of the ts3 human serotonin transporter complexed with fluvoxamine at the central site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for recognition of diverse antidepressants by the human serotonin transporter.

Coleman, J.A.Gouaux, E.

(2018) Nat. Struct. Mol. Biol. 25: 170-175

  • DOI: 10.1038/s41594-018-0026-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Selective serotonin reuptake inhibitors are clinically prescribed antidepressants that act by increasing the local concentrations of neurotransmitters at synapses and in extracellular spaces via blockade of the serotonin transporter. Here we report X ...

    Selective serotonin reuptake inhibitors are clinically prescribed antidepressants that act by increasing the local concentrations of neurotransmitters at synapses and in extracellular spaces via blockade of the serotonin transporter. Here we report X-ray structures of engineered thermostable variants of the human serotonin transporter bound to the antidepressants sertraline, fluvoxamine, and paroxetine. The drugs prevent serotonin binding by occupying the central substrate-binding site and stabilizing the transporter in an outward-open conformation. These structures explain how residues within the central site orchestrate binding of chemically diverse inhibitors and mediate transporter drug selectivity.


    Organizational Affiliation

    Vollum Institute, Oregon Health & Science University, Portland, OR, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium-dependent serotonin transporter
A
549Homo sapiensMutation(s): 5 
Gene Names: SLC6A4 (HTT, SERT)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Solute Carrier (SLC) Transporter Superfamily
Protein: 
Serotonin transporter (SERT) ts3 construct with bound paroxetine at central site
Find proteins for P31645 (Homo sapiens)
Go to Gene View: SLC6A4
Go to UniProtKB:  P31645
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
8B6 antibody FAB heavy chain
B
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
8B6 antibody FAB light chain
C
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FVX
Query on FVX

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Download CCD File 
A
Fluvoxamine
2-[({(1E)-5-methoxy-1-[4-(trifluoromethyl)phenyl]pentylidene}amino)oxy]ethanamine
C15 H21 F3 N2 O2
CJOFXWAVKWHTFT-XSFVSMFZSA-N
 Ligand Interaction
CLR
Query on CLR

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Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.245 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 129.490α = 90.00
b = 163.860β = 90.00
c = 140.950γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental HealthUnited States5R37MH070039

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Author supporting evidence
  • Version 1.2: 2018-01-31
    Type: Database references
  • Version 1.3: 2018-02-14
    Type: Database references
  • Version 1.4: 2018-02-21
    Type: Database references