6W2C

Anomalous iodine signal reveals the position of I-paroxetine complexed with the serotonin transporter at the central site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.30 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.306 
  • R-Value Observed: 0.309 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Chemical and structural investigation of the paroxetine-human serotonin transporter complex.

Coleman, J.A.Navratna, V.Antermite, D.Yang, D.Bull, J.A.Gouaux, E.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.56427
  • Primary Citation of Related Structures:  
    6VRH, 6VRK, 6VRL, 6W2B, 6W2C

  • PubMed Abstract: 

    Antidepressants target the serotonin transporter (SERT) by inhibiting serotonin reuptake. Structural and biochemical studies aiming to understand binding of small-molecules to conformationally dynamic transporters like SERT often require thermostabilizing mutations and antibodies to stabilize a specific conformation, leading to questions about relationships of these structures to the bonafide conformation and inhibitor binding poses of wild-type transporter. To address these concerns, we determined the structures of ∆N72/∆C13 and ts2-inactive SERT bound to paroxetine analogues using single-particle cryo-EM and x-ray crystallography, respectively. We synthesized enantiopure analogues of paroxetine containing either bromine or iodine instead of fluorine. We exploited the anomalous scattering of bromine and iodine to define the pose of these inhibitors and investigated inhibitor binding to Asn177 mutants of ts2-active SERT. These studies provide mutually consistent insights into how paroxetine and its analogues bind to the central substrate-binding site of SERT, stabilize the outward-open conformation, and inhibit serotonin transport.


  • Organizational Affiliation

    Vollum Institute, Oregon Health & Science University, Portland, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium-dependent serotonin transporter549Homo sapiensMutation(s): 0 
Gene Names: SLC6A4HTTSERT
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P31645 (Homo sapiens)
Explore P31645 
Go to UniProtKB:  P31645
PHAROS:  P31645
GTEx:  ENSG00000108576 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31645
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
8B6 heavy chain antibody fragment229Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
8B6 light chain antibody fragment214Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RFY (Subject of Investigation/LOI)
Query on RFY

Download Ideal Coordinates CCD File 
D [auth A]I-paroxetine
C19 H20 I N O3
QJFNUDYGOMCKMV-YOEHRIQHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.30 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.306 
  • R-Value Observed: 0.309 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.99α = 90
b = 159.95β = 90
c = 140.97γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United States5R37MH070039
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2020-09-23
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description