8YR2

Structure of NET-Nisoxetine in outward-open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 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

Dimerization and antidepressant recognition at noradrenaline transporter.

Zhang, H.Yin, Y.L.Dai, A.Zhang, T.Zhang, C.Wu, C.Hu, W.He, X.Pan, B.Jin, S.Yuan, Q.Wang, M.W.Yang, D.Xu, H.E.Jiang, Y.

(2024) Nature 630: 247-254

  • DOI: https://doi.org/10.1038/s41586-024-07437-6
  • Primary Citation of Related Structures:  
    8Y8Z, 8Y90, 8Y91, 8Y92, 8Y93, 8Y94, 8Y95, 8YR2

  • PubMed Abstract: 

    The noradrenaline transporter has a pivotal role in regulating neurotransmitter balance and is crucial for normal physiology and neurobiology 1 . Dysfunction of noradrenaline transporter has been implicated in numerous neuropsychiatric diseases, including depression and attention deficit hyperactivity disorder 2 . Here we report cryo-electron microscopy structures of noradrenaline transporter in apo and substrate-bound forms, and as complexes with six antidepressants. The structures reveal a noradrenaline transporter dimer interface that is mediated predominantly by cholesterol and lipid molecules. The substrate noradrenaline binds deep in the central binding pocket, and its amine group interacts with a conserved aspartate residue. Our structures also provide insight into antidepressant recognition and monoamine transporter selectivity. Together, these findings advance our understanding of noradrenaline transporter regulation and inhibition, and provide templates for designing improved antidepressants to treat neuropsychiatric disorders.


  • Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium-dependent noradrenaline transporterA [auth B],
B [auth A]
617Homo sapiensMutation(s): 0 
Gene Names: SLC6A2NAT1NET1SLC6A5
UniProt & NIH Common Fund Data Resources
Find proteins for P23975 (Homo sapiens)
Explore P23975 
Go to UniProtKB:  P23975
GTEx:  ENSG00000103546 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23975
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIO
Query on PIO

Download Ideal Coordinates CCD File 
D [auth B],
V [auth A]
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
A1LX7 (Subject of Investigation/LOI)
Query on A1LX7

Download Ideal Coordinates CCD File 
EA [auth A],
FA [auth A],
O [auth B],
P [auth B]
[(2R)-2-octanoyloxy-3-[oxidanyl-[(2R,3R,5S,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H47 O13 P
UPUKKDCTWWVPCJ-OZRWLNDDSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
GA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
GA [auth A],
H [auth B],
HA [auth A],
I [auth B],
IA [auth A],
J [auth B],
JA [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
Z [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
41U
Query on 41U

Download Ideal Coordinates CCD File 
C [auth B],
U [auth A]
nisoxetine
C17 H21 N O2
ITJNARMNRKSWTA-HNNXBMFYSA-N
CL
Query on CL

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

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B],
W [auth A],
X [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Database references
  • Version 1.3: 2024-06-26
    Changes: Data collection, Database references
  • Version 1.4: 2024-07-03
    Changes: Data collection, Database references