5I74

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.395 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structures and mechanism of the human serotonin transporter.

Coleman, J.A.Green, E.M.Gouaux, E.

(2016) Nature 532: 334-339

  • DOI: 10.1038/nature17629
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The serotonin transporter (SERT) terminates serotonergic signalling through the sodium- and chloride-dependent reuptake of neurotransmitter into presynaptic neurons. SERT is a target for antidepressant and psychostimulant drugs, which block reuptake ...

    The serotonin transporter (SERT) terminates serotonergic signalling through the sodium- and chloride-dependent reuptake of neurotransmitter into presynaptic neurons. SERT is a target for antidepressant and psychostimulant drugs, which block reuptake and prolong neurotransmitter signalling. Here we report X-ray crystallographic structures of human SERT at 3.15 Å resolution bound to the antidepressants (S)-citalopram or paroxetine. Antidepressants lock SERT in an outward-open conformation by lodging in the central binding site, located between transmembrane helices 1, 3, 6, 8 and 10, directly blocking serotonin binding. We further identify the location of an allosteric site in the complex as residing at the periphery of the extracellular vestibule, interposed between extracellular loops 4 and 6 and transmembrane helices 1, 6, 10 and 11. Occupancy of the allosteric site sterically hinders ligand unbinding from the central site, providing an explanation for the action of (S)-citalopram as an allosteric ligand. These structures define the mechanism of antidepressant action in SERT, and provide blueprints for future drug design.


    Organizational Affiliation

    Vollum Institute, Oregon Health &Science University, Portland, Oregon 97239, 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, heavy chain
B
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
8B6 antibody, 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
69D
Query on 69D

Download SDF File 
Download CCD File 
A
(1S)-1-(4-bromophenyl)-1-[3-(dimethylamino)propyl]-1,3-dihydro-2-benzofuran-5-carbonitrile
C20 H21 Br N2 O
SOYXTZZNZQFLGF-FQEVSTJZSA-N
 Ligand Interaction
D12
Query on D12

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Download CCD File 
A
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 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
HEX
Query on HEX

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Download CCD File 
A
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-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: 3.395 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.249 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 129.590α = 90.00
b = 164.000β = 90.00
c = 140.170γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references
  • Version 1.2: 2016-05-04
    Type: Database references