9EUO

Outward-open structure of Drosophila dopamine transporter bound to an atypical non-competitive inhibitor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium-dependent dopamine transporter543Drosophila melanogasterMutation(s): 5 
Gene Names: DATfmnCG8380
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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
9D5 ANTIBODY, LIGHT CHAINB [auth L]237Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
9D5 ANTIBODY, HEAVY CHAINC [auth H]240Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01
Query on Y01

Download Ideal Coordinates CCD File 
E [auth A]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
A1H8F (Subject of Investigation/LOI)
Query on A1H8F

Download Ideal Coordinates CCD File 
D [auth A]N-[3-(6-chloranyl-1,3,4,9-tetrahydropyrido[3,4-b]indol-2-yl)propyl]butanamide
C18 H24 Cl N3 O
AUJJZIKBHNXABX-UHFFFAOYSA-N
144
Query on 144

Download Ideal Coordinates CCD File 
F [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 
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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: 2024-10-09
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references