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 9EUP | pdb_00009eup

Inhibitor-free outward-open structure of Drosophila dopamine transporter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9EUP

This is version 1.2 of the entry. See complete history. 

Literature

Cryo-EM structure of the dopamine transporter with a novel atypical non-competitive inhibitor bound to the orthosteric site.

Pedersen, C.N., Yang, F., Ita, S., Xu, Y., Akunuri, R., Trampari, S., Neumann, C.M.T., Desdorf, L.M., Schiott, B., Salvino, J.M., Mortensen, O.V., Nissen, P., Shahsavar, A.

(2024) J Neurochem 168: 2043-2055

  • DOI: https://doi.org/10.1111/jnc.16179
  • Primary Citation Related Structures: 
    9EUO, 9EUP

  • PubMed Abstract: 

    The regulation of dopamine (DA) removal from the synaptic cleft is a crucial process in neurotransmission and is facilitated by the sodium- and chloride-coupled dopamine transporter DAT. Psychostimulant drugs, cocaine, and amphetamine, both block the uptake of DA, while amphetamine also triggers the release of DA. As a result, they prolong or even amplify neurotransmitter signaling. Atypical inhibitors of DAT lack cocaine-like rewarding effects and offer a promising strategy for the treatment of drug use disorders. Here, we present the 3.2 Å resolution cryo-electron microscopy structure of the Drosophila melanogaster dopamine transporter (dDAT) in complex with the atypical non-competitive inhibitor AC-4-248. The inhibitor partially binds at the central binding site, extending into the extracellular vestibule, and locks the transporter in an outward open conformation. Our findings propose mechanisms for the non-competitive inhibition of DAT and attenuation of cocaine potency by AC-4-248 and provide a basis for the rational design of more efficacious atypical inhibitors.


  • Organizational Affiliation: 
    • DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.

Macromolecule Content 

  • Total Structure Weight: 113.78 kDa 
  • Atom Count: 7,602 
  • Modeled Residue Count: 965 
  • Deposited Residue Count: 1,020 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium-dependent dopamine transporter543Drosophila melanogasterMutation(s): 5 
Gene Names: DAT, fmn, CG8380
Membrane Entity: Yes 
UniProt
Find proteins for Q7K4Y6 (Drosophila melanogaster)
Explore Q7K4Y6 
Go to UniProtKB:  Q7K4Y6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7K4Y6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
9D5 ANTIBODY, HEAVY CHAINB [auth H]240Mus musculusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
9D5 ANTIBODY, LIGHT CHAINC [auth L]237Mus musculusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01

Query on Y01



Download:Ideal Coordinates CCD File
D [auth A]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
F [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
144

Query on 144



Download:Ideal Coordinates CCD File
E [auth A]TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
C4 H12 N O3
DRDCQJADRSJFFD-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF19OC0054875
LundbeckfondenDenmarkR310-2018-3713
Danish Ministry for Research and Higher EducationDenmark5072-00025B
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesMH121453
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesMH106912
LundbeckfondenDenmarkR368-2021-522
Novo Nordisk FoundationDenmarkNNF18OC0032608
Aarhus University Research FoundationDenmarkAUFF-E-2022-9-24
National Institutes of Health/National Library of Medicine (NIH/NLM)United StatesR01 DA051205-03
National Institutes of Health/National Library of Medicine (NIH/NLM)United StatesS10OD030245-01
National Institutes of Health/National Library of Medicine (NIH/NLM)United StatesP30 CA010815-53

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-20
    Changes: Data collection