4XPT

X-ray structure of Drosophila dopamine transporter with subsiteB mutations D121G/S426M and EL2 deletion of 162-201 in complex with substrate analogue 3,4 dichlorophen ethylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Neurotransmitter and psychostimulant recognition by the dopamine transporter.

Wang, K.H.Penmatsa, A.Gouaux, E.

(2015) Nature 521: 322-327

  • DOI: 10.1038/nature14431
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Na(+)/Cl(-)-coupled biogenic amine transporters are the primary targets of therapeutic and abused drugs, ranging from antidepressants to the psychostimulants cocaine and amphetamines, and to their cognate substrates. Here we determine X-ray crystal s ...

    Na(+)/Cl(-)-coupled biogenic amine transporters are the primary targets of therapeutic and abused drugs, ranging from antidepressants to the psychostimulants cocaine and amphetamines, and to their cognate substrates. Here we determine X-ray crystal structures of the Drosophila melanogaster dopamine transporter (dDAT) bound to its substrate dopamine, a substrate analogue 3,4-dichlorophenethylamine, the psychostimulants d-amphetamine and methamphetamine, or to cocaine and cocaine analogues. All ligands bind to the central binding site, located approximately halfway across the membrane bilayer, in close proximity to bound sodium and chloride ions. The central binding site recognizes three chemically distinct classes of ligands via conformational changes that accommodate varying sizes and shapes, thus illustrating molecular principles that distinguish substrates from inhibitors in biogenic amine transporters.


    Organizational Affiliation

    Vollum Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dopamine transporter
A
535Drosophila melanogasterMutation(s): 4 
Gene Names: DAT (fmn)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Solute Carrier (SLC) Transporter Superfamily
Protein: 
DAT Dopamine transporter in complex with nortriptyline TCA (tricyclic antidepressant)
Find proteins for Q7K4Y6 (Drosophila melanogaster)
Go to UniProtKB:  Q7K4Y6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
antibody fragment light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
antibody fragment heavy chain
H
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y01
Query on Y01

Download SDF File 
Download CCD File 
A
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
N9S
Query on N9S

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Download CCD File 
A
4-O-alpha-D-Glucopyranosyl-beta-D-glucopyranose
Beta-Maltose
C12 H22 O11
GUBGYTABKSRVRQ-QUYVBRFLSA-N
 Ligand Interaction
42J
Query on 42J

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Download CCD File 
A
2-(3,4-dichlorophenyl)ethanamine
C8 H9 Cl2 N
MQPUAVYKVIHUJP-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-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: 3.36 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.614α = 90.00
b = 139.148β = 90.00
c = 166.679γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-27
    Type: Database references
  • Version 1.2: 2015-06-03
    Type: Database references
  • Version 1.3: 2015-10-14
    Type: Other
  • Version 1.4: 2017-11-22
    Type: Derived calculations, Refinement description