6NLE | pdb_00006nle

X-ray structure of LeuT with V269 deletion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 
    0.260 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6NLE

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural, functional, and behavioral insights of dopamine dysfunction revealed by a deletion inSLC6A3.

Campbell, N.G.Shekar, A.Aguilar, J.I.Peng, D.Navratna, V.Yang, D.Morley, A.N.Duran, A.M.Galli, G.O'Grady, B.Ramachandran, R.Sutcliffe, J.S.Sitte, H.H.Erreger, K.Meiler, J.Stockner, T.Bellan, L.M.Matthies, H.J.G.Gouaux, E.Mchaourab, H.S.Galli, A.

(2019) Proc Natl Acad Sci U S A 116: 3853-3862

  • DOI: https://doi.org/10.1073/pnas.1816247116
  • Primary Citation Related Structures: 
    6NLE

  • PubMed Abstract: 

    The human dopamine (DA) transporter (hDAT) mediates clearance of DA. Genetic variants in hDAT have been associated with DA dysfunction, a complication associated with several brain disorders, including autism spectrum disorder (ASD). Here, we investigated the structural and behavioral bases of an ASD-associated in-frame deletion in hDAT at N336 (∆N336). We uncovered that the deletion promoted a previously unobserved conformation of the intracellular gate of the transporter, likely representing the rate-limiting step of the transport process. It is defined by a "half-open and inward-facing" state (HOIF) of the intracellular gate that is stabilized by a network of interactions conserved phylogenetically, as we demonstrated in hDAT by Rosetta molecular modeling and fine-grained simulations, as well as in its bacterial homolog leucine transporter by electron paramagnetic resonance analysis and X-ray crystallography. The stabilization of the HOIF state is associated both with DA dysfunctions demonstrated in isolated brains of Drosophila melanogaster expressing hDAT ∆N336 and with abnormal behaviors observed at high-time resolution. These flies display increased fear, impaired social interactions, and locomotion traits we associate with DA dysfunction and the HOIF state. Together, our results describe how a genetic variation causes DA dysfunction and abnormal behaviors by stabilizing a HOIF state of the transporter.


  • Organizational Affiliation
    • Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232.

Macromolecule Content 

  • Total Structure Weight: 57.9 kDa 
  • Atom Count: 4,000 
  • Modeled Residue Count: 491 
  • Deposited Residue Count: 504 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Na(+):neurotransmitter symporter (Snf family)504Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: snfaq_2077
Membrane Entity: Yes 
UniProt
Find proteins for O67854 (Aquifex aeolicus (strain VF5))
Explore O67854 
Go to UniProtKB:  O67854
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67854
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BOG

Query on BOG



Download:Ideal Coordinates CCD File
L [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
LEU

Query on LEU



Download:Ideal Coordinates CCD File
B [auth A]LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
OCT

Query on OCT



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free:  0.260 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.54α = 90
b = 86.14β = 110.72
c = 81.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Structure summary