6XWM

Mechanism of substrate release in neurotransmitter:sodium symporters: the structure of LeuT in an inward-facing occluded conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

X-ray structure of LeuT in an inward-facing occluded conformation reveals mechanism of substrate release.

Gotfryd, K.Boesen, T.Mortensen, J.S.Khelashvili, G.Quick, M.Terry, D.S.Missel, J.W.LeVine, M.V.Gourdon, P.Blanchard, S.C.Javitch, J.A.Weinstein, H.Loland, C.J.Nissen, P.Gether, U.

(2020) Nat Commun 11: 1005-1005

  • DOI: https://doi.org/10.1038/s41467-020-14735-w
  • Primary Citation of Related Structures:  
    6XWM

  • PubMed Abstract: 

    Neurotransmitter:sodium symporters (NSS) are conserved from bacteria to man and serve as targets for drugs, including antidepressants and psychostimulants. Here we report the X-ray structure of the prokaryotic NSS member, LeuT, in a Na + /substrate-bound, inward-facing occluded conformation. To obtain this structure, we were guided by findings from single-molecule fluorescence spectroscopy and molecular dynamics simulations indicating that L-Phe binding and mutation of the conserved N-terminal Trp8 to Ala both promote an inward-facing state. Compared to the outward-facing occluded conformation, our structure reveals a major tilting of the cytoplasmic end of transmembrane segment (TM) 5, which, together with release of the N-terminus but without coupled movement of TM1, opens a wide cavity towards the second Na + binding site. The structure of this key intermediate in the LeuT transport cycle, in the context of other NSS structures, leads to the proposal of an intracellular release mechanism of substrate and ions in NSS proteins.


  • Organizational Affiliation

    Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-5, DK-2200, Copenhagen N, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Na(+):neurotransmitter symporter (Snf family)
A, B
519Aquifex 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.848α = 65.38
b = 83.985β = 89.77
c = 86.939γ = 64.56
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR133-A12689
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesP01 DA012408
LundbeckfondenDenmark2009-4585
LundbeckfondenDenmarkDANDRITE-R248-2016-2518
The Carlsberg FoundationDenmarkCF17-0171
Danish Council for Independent ResearchDenmarkSapere Aude 0602-02100B
Danish Council for Independent ResearchDenmarkFP1 0602-02100B
Danish Council for Independent ResearchDenmark4183-00581
European Communitys Seventh Framework ProgrammeEuropean UnionFP7/2007-2013 HEALTH-F4-2007- 201924

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Derived calculations, Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description