LeuT T354H mutant in the outward-oriented, Na+-free Return State

Experimental Data Snapshot

  • Resolution: 2.58 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

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


A conserved leucine occupies the empty substrate site of LeuT in the Na(+)-free return state.

Malinauskaite, L.Said, S.Sahin, C.Grouleff, J.Shahsavar, A.Bjerregaard, H.Noer, P.Severinsen, K.Boesen, T.Schitt, B.Sinning, S.Nissen, P.

(2016) Nat Commun 7: 11673-11673

  • DOI: https://doi.org/10.1038/ncomms11673
  • Primary Citation of Related Structures:  
    5JAE, 5JAF, 5JAG

  • PubMed Abstract: 

    Bacterial members of the neurotransmitter:sodium symporter (NSS) family perform Na(+)-dependent amino-acid uptake and extrude H(+) in return. Previous NSS structures represent intermediates of Na(+)/substrate binding or intracellular release, but not the inward-to-outward return transition. Here we report crystal structures of Aquifex aeolicus LeuT in an outward-oriented, Na(+)- and substrate-free state likely to be H(+)-occluded. We find a remarkable rotation of the conserved Leu25 into the empty substrate-binding pocket and rearrangements of the empty Na(+) sites. Mutational studies of the equivalent Leu99 in the human serotonin transporter show a critical role of this residue on the transport rate. Molecular dynamics simulations show that extracellular Na(+) is blocked unless Leu25 is rotated out of the substrate-binding pocket. We propose that Leu25 facilitates the inward-to-outward transition by compensating a Na(+)- and substrate-free state and acts as the gatekeeper for Na(+) binding that prevents leak in inward-outward return transitions.

  • Organizational Affiliation

    Danish Research Institute of Translational Neuroscience-DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus C DK-8000, Denmark.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transporter519Aquifex aeolicus VF5Mutation(s): 1 
Gene Names: snfaq_2077
Membrane Entity: Yes 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.58 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.23α = 90
b = 95.61β = 97.81
c = 83.7γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Lundbeck FoundationDenmark2012-12576

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary