5I6X

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

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
  • Primary Citation of Related Structures:  
    5I66, 5I6Z, 5I74, 5I73, 5I75, 5I6X, 5I71

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
8B6 antibody, heavy chainB221Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
8B6 antibody, light chainC214Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download CCD File 
A
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
CLR
Query on CLR

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A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
8PR
Query on 8PR

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A
Paroxetine
C19 H20 F N O3
AHOUBRCZNHFOSL-YOEHRIQHSA-N
 Ligand Interaction
NAG
Query on NAG

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A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8PRKi:  0.07999999821186066   nM  BindingDB
8PRIC50:  0.2800000011920929   nM  BindingDB
8PRKi:  0.5299999713897705   nM  BindingDB
8PRKi:  0.10000000149011612   nM  BindingDB
8PRKi:  0.05000000074505806   nM  BindingDB
8PRKi:  0.800000011920929   nM  BindingDB
8PRKi:  0.10999999940395355   nM  BindingDB
8PRIC50:  0.5600000023841858   nM  BindingDB
8PRKi:  0.3400000035762787   nM  BindingDB
8PRKi:  0.12999999523162842   nM  BindingDB
8PRKd:  0.12999999523162842   nM  BindingDB
8PRKi:  0.47999998927116394   nM  BindingDB
8PRIC50:  6.429999828338623   nM  BindingDB
8PRKd:  0.15000000596046448   nM  BindingDB
8PRKi:  0.019999999552965164   nM  BindingDB
8PRKi:  0.41999998688697815   nM  BindingDB
8PRKi:  0.28999999165534973   nM  BindingDB
8PRIC50:  0.20000000298023224   nM  BindingDB
8PRKi:  0.09000000357627869   nM  BindingDB
8PRKi:  0.03999999910593033   nM  BindingDB
8PRKi:  4.699999809265137   nM  BindingDB
8PRKi:  0.03999999910593033   nM  BindingDB
8PRKi:  0.4399999976158142   nM  BindingDB
8PRIC50:  2   nM  BindingDB
8PRKi:  0.699999988079071   nM  BindingDB
8PRKi:  0.7300000190734863   nM  BindingDB
8PRKi:  0.05999999865889549   nM  BindingDB
8PRKi:  0.3799999952316284   nM  BindingDB
8PRKi:  0.8299999833106995   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.15α = 90
b = 162.83β = 90
c = 140.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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