4XNX

X-ray structure of Drosophila dopamine transporter in complex with reboxetine

• PDB DOI: https://doi.org/10.2210/pdb4XNX/pdb

• Classification: transport protein/inhibitor
• Organism(s): Drosophila melanogaster, Mus musculus
• Expression System: Homo sapiens, Mus musculus
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2015-01-16 Released: 2015-05-13 
• Deposition Author(s): Aravind, P., Wang, K., Gouaux, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

X-ray structures of Drosophila dopamine transporter in complex with nisoxetine and reboxetine.

Penmatsa, A., Wang, K.H., Gouaux, E.

(2015) Nat Struct Mol Biol 22: 506-508

• PubMed: 25961798 
• DOI: https://doi.org/10.1038/nsmb.3029
• Primary Citation of Related Structures:  
  4XNU, 4XNX


• PubMed Abstract: 
  

  Most antidepressants elicit their therapeutic benefits through selective blockade of Na(+)/Cl(-)-coupled neurotransmitter transporters. Here we report X-ray structures of the Drosophila melanogaster dopamine transporter in complexes with the polycyclic antidepressants nisoxetine or reboxetine. The inhibitors stabilize the transporter in an outward-open conformation by occupying the substrate-binding site. These structures explain how interactions between the binding pocket and substituents on the aromatic rings of antidepressants modulate drug-transporter selectivity.

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Organizational Affiliation: 

Vollum Institute, Oregon Health & Science University, Portland OR.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 110.89 kDa 
• Atom Count: 7,514 
• Modelled Residue Count: 966 
• Deposited Residue Count: 990 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transporter	A	536	Drosophila melanogaster	Mutation(s): 2  Gene Names: DAT, Dmel_CG8380 Membrane Entity: Yes
UniProt
Find proteins for Q7K4Y6 (Drosophila melanogaster) Explore Q7K4Y6  Go to UniProtKB:  Q7K4Y6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody fragment light chain	B [auth L]	214	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody fragment heavy chain	C [auth H]	240	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	D [auth B]	2		N/A
Glycosylation Resources
GlyTouCan:  G66120GK GlyCosmos:  G66120GK

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	E [auth A], F [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
41X	J [auth A]	(2R)-2-[(R)-(2-ethoxyphenoxy)(phenyl)methyl]morpholine C19 H23 N O3 CBQGYUDMJHNJBX-RTBURBONSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900018	D [auth B]	beta-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.673	α = 90
b = 141.036	β = 90
c = 167.247	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Aravind, P., Wang, K., Gouaux, E.

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2015-05-27
  Changes: Database references
• Version 1.2: 2015-06-10
  Changes: Database references
• Version 1.3: 2017-05-31
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary