8VBY

Structure of the human dopamine transporter in complex with beta-CFT, MRS7292 and divalent zinc

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 
  • Membrane Protein: Yes  mpstruc

  • Deposited: 2023-12-12 Released: 2024-08-07 
  • Deposition Author(s): Srivastava, D.K., Gouaux, E.
  • Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of the human dopamine transporter and mechanisms of inhibition.

Srivastava, D.K.Navratna, V.Tosh, D.K.Chinn, A.Sk, M.F.Tajkhorshid, E.Jacobson, K.A.Gouaux, E.

(2024) Nature 632: 672-677

  • DOI: https://doi.org/10.1038/s41586-024-07739-9
  • Primary Citation of Related Structures:  
    8VBY

  • PubMed Abstract: 

    The neurotransmitter dopamine has central roles in mood, appetite, arousal and movement 1 . Despite its importance in brain physiology and function, and as a target for illicit and therapeutic drugs, the human dopamine transporter (hDAT) and mechanisms by which it is inhibited by small molecules and Zn 2+ are without a high-resolution structural context. Here we determine the structure of hDAT in a tripartite complex with the competitive inhibitor and cocaine analogue, (-)-2-β-carbomethoxy-3-β-(4-fluorophenyl)tropane 2 (β-CFT), the non-competitive inhibitor MRS7292 3 and Zn 2 + (ref. 4 ). We show how β-CFT occupies the central site, approximately halfway across the membrane, stabilizing the transporter in an outward-open conformation. MRS7292 binds to a structurally uncharacterized allosteric site, adjacent to the extracellular vestibule, sequestered underneath the extracellular loop 4 (EL4) and adjacent to transmembrane helix 1b (TM1b), acting as a wedge, precluding movement of TM1b and closure of the extracellular gate. A Zn 2+ ion further stabilizes the outward-facing conformation by coupling EL4 to EL2, TM7 and TM8, thus providing specific insights into how Zn 2+ restrains the movement of EL4 relative to EL2 and inhibits transport activity.


  • Organizational Affiliation

    Vollum Institute, Oregon Health and Science University, Portland, OR, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium-dependent dopamine transporter571Homo sapiensMutation(s): 1 
Gene Names: SLC6A3
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q01959-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01
Query on Y01

Download Ideal Coordinates CCD File 
E [auth A],
K [auth A],
L [auth A],
MA [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
A1AAF (Subject of Investigation/LOI)
Query on A1AAF

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C [auth A]methyl (1S,2R,3S,4R,5R)-4-{2-[(5-chlorothiophen-2-yl)ethynyl]-6-(methylamino)-9H-purin-9-yl}-2,3-dihydroxybicyclo[3.1.0]hexane-1-carboxylate
C20 H18 Cl N5 O4 S
OXHKHNQYCDYUIU-LJARFEBYSA-N
42L (Subject of Investigation/LOI)
Query on 42L

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B [auth A]methyl (1R,2S,3S,5S)-3-(4-fluorophenyl)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate
C16 H20 F N O2
QUSLQENMLDRCTO-YJNKXOJESA-N
NAG
Query on NAG

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D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MYS
Query on MYS

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Z [auth A]PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
D12
Query on D12

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AA [auth A]
CA [auth A]
KA [auth A]
NA [auth A]
Q [auth A]
AA [auth A],
CA [auth A],
KA [auth A],
NA [auth A],
Q [auth A],
R [auth A]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10
Query on D10

Download Ideal Coordinates CCD File 
F [auth A]
H [auth A]
IA [auth A]
JA [auth A]
OA [auth A]
F [auth A],
H [auth A],
IA [auth A],
JA [auth A],
OA [auth A],
PA [auth A],
S [auth A],
Y [auth A]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT
Query on OCT

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DA [auth A],
EA [auth A]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HP6
Query on HP6

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BA [auth A]
FA [auth A]
HA [auth A]
LA [auth A]
M [auth A]
BA [auth A],
FA [auth A],
HA [auth A],
LA [auth A],
M [auth A],
P [auth A],
T [auth A],
U [auth A]
HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N
LNK
Query on LNK

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G [auth A]
GA [auth A]
I [auth A]
J [auth A]
V [auth A]
G [auth A],
GA [auth A],
I [auth A],
J [auth A],
V [auth A],
W [auth A],
X [auth A]
PENTANE
C5 H12
OFBQJSOFQDEBGM-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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N [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

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O [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United States5R01MH070039
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Data collection, Structure summary
  • 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: 2024-09-04
    Changes: Data collection, Database references
  • Version 1.5: 2024-10-23
    Changes: Data collection, Structure summary