6AWN | pdb_00006awn

X-ray structure of the S439T human serotonin transporter complexed with paroxetine at the central site

PDB DOI: https://doi.org/10.2210/pdb6AWN/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens, Mus musculus
Expression System: Homo sapiens, Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2017-09-06 Released: 2017-10-25
Deposition Author(s): Coleman, J.A., Gouaux, E.
Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.62 Å
R-Value Free:
0.263 (Depositor), 0.274 (DCC)
R-Value Work:
0.256 (Depositor), 0.258 (DCC)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.9 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

PubMed: 29379174 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-018-0026-8
Primary Citation Related Structures:
6AWN, 6AWO, 6AWP, 6AWQ

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-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.

Macromolecule Content

Total Structure Weight: 112 kDa
Atom Count: 7,703
Modeled Residue Count: 976
Deposited Residue Count: 992
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-dependent serotonin transporter	A	549	Homo sapiens	Mutation(s): 4 Gene Names: SLC6A4, HTT, SERT 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31645
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: P31645-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
8B6 antibody FAB heavy chain	B	229	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A0F7R1P3 (Mus musculus) Explore A0A0F7R1P3 Go to UniProtKB: A0A0F7R1P3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0F7R1P3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
8B6 antibody FAB light chain	C	214	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A0F7R5U8 (Mus musculus) Explore A0A0F7R5U8 Go to UniProtKB: A0A0F7R5U8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0F7R5U8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
8PR Query on 8PR Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	Paroxetine C₁₉ H₂₀ F N O₃ AHOUBRCZNHFOSL-YOEHRIQHSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	D [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
8PR	BindingDB: 6AWN	Ki: min: 0.02, max: 0.83 (nM) from 23 assay(s)
		Kd: min: 0.13, max: 0.15 (nM) from 2 assay(s)
		IC50: min: 0.2, max: 6.43 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.62 Å
R-Value Free: 0.263 (Depositor), 0.274 (DCC)
R-Value Work: 0.256 (Depositor), 0.258 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.15	α = 90
b = 162.84	β = 90
c = 140.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-10-25

Deposition Author(s):

Coleman, J.A.

Gouaux, E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	5R37MH070039

Revision History (Full details and data files)

Version 1.0: 2017-10-25
Type: Initial release
Version 1.1: 2017-11-22
Changes: Database references
Version 1.2: 2017-12-06
Changes: Author supporting evidence
Version 1.3: 2018-01-31
Changes: Database references
Version 1.4: 2018-02-14
Changes: Database references
Version 1.5: 2018-02-21
Changes: Database references
Version 1.6: 2019-11-27
Changes: Author supporting evidence
Version 1.7: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.8: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.9: 2024-10-09
Changes: Structure summary