5I75

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Structures With Same Primary Citation

  • 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

    Howard Hughes Medical Institute, Oregon Health &Science University, Portland, Oregon 97239, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
8B6 antibody, light chainC214Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium-dependent serotonin transporterA549Homo sapiensMutation(s): 4 
Gene Names: SLC6A4HTTSERT
Membrane protein
Mpstruc
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)
Explore P31645 
Go to UniProtKB:  P31645
NIH Common Fund Data Resources
PHAROS  P31645
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
8B6 antibody, heavy chainB221Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
69D
Query on 69D

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
68P
Query on 68P

Download CCD File 
A
(1S)-1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile
C20 H21 F N2 O
WSEQXVZVJXJVFP-FQEVSTJZSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
C14
Query on C14

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A
TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
68PKi:  1.940000057220459   nM  BindingDB
68PKi:  2.5   nM  BindingDB
68PKi:  7.400000095367432   nM  BindingDB
68PKi:  1.5   nM  BindingDB
68PIC50:  19   nM  BindingDB
68PKi:  0.8899999856948853   nM  BindingDB
68PIC50:  1.7999999523162842   nM  BindingDB
68PKd:  2.5999999046325684   nM  BindingDB
68PKi:  0.8199999928474426   nM  BindingDB
68PKi:  2.7100000381469727   nM  BindingDB
68PKi:  1.100000023841858   nM  BindingDB
68PIC50:  2.0999999046325684   nM  BindingDB
68PKi:  1.159999966621399   nM  BindingDB
68PIC50:  3.9000000953674316   nM  BindingDB
68PKi:  1.600000023841858   nM  BindingDB
68PKi:  0.75   nM  BindingDB
68PIC50:  3.1700000762939453   nM  BindingDB
68PEC50:  5100   nM  BindingDB
68PKi:  32.79999923706055   nM  BindingDB
68PEC50:  5800   nM  BindingDB
68PKi:  2.200000047683716   nM  BindingDB
68PKi:  0.6499999761581421   nM  BindingDB
68PKi:  1.600000023841858   nM  BindingDB
68PKi:  1   nM  BindingDB
68PKi:  16   nM  BindingDB
68PKi:  19   nM  BindingDB
68PKi:  2.4000000953674316   nM  BindingDB
68PKi:  3.509999990463257   nM  BindingDB
68PKi:  1.5   nM  BindingDB
68PKi:  1.7999999523162842   nM  BindingDB
68PKi:  1.1299999952316284   nM  BindingDB
68PKi:  9.199999809265137   nM  BindingDB
68PKi:  0.7799999713897705   nM  BindingDB
68PIC50:  10   nM  BindingDB
68PEC50:  8700   nM  BindingDB
68PKi:  8.899999618530273   nM  BindingDB
68PIC50:  6.699999809265137   nM  BindingDB
68PKi:  4.380000114440918   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.6α = 90
b = 163.41β = 90
c = 140.47γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2016-05-04
    Changes: Database references
  • Version 1.3: 2020-03-04
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary