9EO4

Outward-open structure of human dopamine transporter bound to cocaine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the human dopamine transporter in complex with cocaine.

Nielsen, J.C.Salomon, K.Kalenderoglou, I.E.Bargmeyer, S.Pape, T.Shahsavar, A.Loland, C.J.

(2024) Nature 632: 678-685

  • DOI: https://doi.org/10.1038/s41586-024-07804-3
  • Primary Citation of Related Structures:  
    9EO4

  • PubMed Abstract: 

    The dopamine transporter (DAT) is crucial for regulating dopamine signalling and is the prime mediator for the rewarding and addictive effects of cocaine 1 . As part of the neurotransmitter sodium symporter family, DAT uses the Na + gradient across cell membranes to transport dopamine against its chemical gradient 2 . The transport mechanism involves both intra- and extracellular gates that control substrate access to a central site. However, the molecular intricacies of this process and the inhibitory mechanism of cocaine have remained unclear. Here, we present the molecular structure of human DAT in complex with cocaine at a resolution of 2.66 Å. Our findings reveal that DAT adopts the expected LeuT-fold, posing in an outward-open conformation with cocaine bound at the central (S1) site. Notably, while an Na + occupies the second Na + site (Na2), the Na1 site seems to be vacant, with the side chain of Asn82 occupying the presumed Na + space. This structural insight elucidates the mechanism for the cocaine inhibition of human DAT and deepens our understanding of neurotransmitter transport. By shedding light on the molecular underpinnings of how cocaine acts, our study lays a foundation for the development of targeted medications to combat addiction.


  • Organizational Affiliation

    Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium-dependent dopamine transporterA [auth B]660Homo sapiensMutation(s): 0 
Gene Names: SLC6A3DAT1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q01959 (Homo sapiens)
Explore Q01959 
Go to UniProtKB:  Q01959
PHAROS:  Q01959
GTEx:  ENSG00000142319 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01959
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 
C [auth B]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
B,
D [auth B],
E [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
COC (Subject of Investigation/LOI)
Query on COC

Download Ideal Coordinates CCD File 
H [auth B]COCAINE
C17 H21 N O4
ZPUCINDJVBIVPJ-LJISPDSOSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
COC BindingDB:  9EO4 Ki: min: 68.5, max: 1270 (nM) from 38 assay(s)
IC50: min: 65, max: 1.58e+4 (nM) from 22 assay(s)
EC50: min: 267, max: 303 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR344-2020-1020
The Carlsberg FoundationDenmarkCF20-0345
Independent Research Fund Denmark - Technology and Production SciencesDenmark3101-00381B
H2020 Marie Curie Actions of the European CommissionEuropean Union860954
Maersk FoundationDenmarkL-2022-00324
Maersk FoundationDenmarkL-2021-00122

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-08-21
    Changes: Data collection, Database references
  • Version 1.3: 2024-08-28
    Changes: Data collection, Database references
  • Version 1.4: 2024-11-13
    Changes: Data collection, Structure summary