3TT3

Crystal Structure of LeuT in the inward-open conformation in complex with Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

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This is version 1.5 of the entry. See complete history


Literature

X-ray structures of LeuT in substrate-free outward-open and apo inward-open states.

Krishnamurthy, H.Gouaux, E.

(2012) Nature 481: 469-474

  • DOI: https://doi.org/10.1038/nature10737
  • Primary Citation of Related Structures:  
    3TT1, 3TT3, 3TU0

  • PubMed Abstract: 

    Neurotransmitter sodium symporters are integral membrane proteins that remove chemical transmitters from the synapse and terminate neurotransmission mediated by serotonin, dopamine, noradrenaline, glycine and GABA (γ-aminobutyric acid). Crystal structures of the bacterial homologue, LeuT, in substrate-bound outward-occluded and competitive inhibitor-bound outward-facing states have advanced our mechanistic understanding of neurotransmitter sodium symporters but have left fundamental questions unanswered. Here we report crystal structures of LeuT mutants in complexes with conformation-specific antibody fragments in the outward-open and inward-open states. In the absence of substrate but in the presence of sodium the transporter is outward-open, illustrating how the binding of substrate closes the extracellular gate through local conformational changes: hinge-bending movements of the extracellular halves of transmembrane domains 1, 2 and 6, together with translation of extracellular loop 4. The inward-open conformation, by contrast, involves large-scale conformational changes, including a reorientation of transmembrane domains 1, 2, 5, 6 and 7, a marked hinge bending of transmembrane domain 1a and occlusion of the extracellular vestibule by extracellular loop 4. These changes close the extracellular gate, open an intracellular vestibule, and largely disrupt the two sodium sites, thus providing a mechanism by which ions and substrate are released to the cytoplasm. The new structures establish a structural framework for the mechanism of neurotransmitter sodium symporters and their modulation by therapeutic and illicit substances.


  • Organizational Affiliation

    Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine transporter LeuT519Aquifex aeolicusMutation(s): 4 
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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mouse monoclonal 1gG1 Fab fragment, heavy chainB [auth L]218Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
mouse monoclonal 1gG1 Fab fragment, kappa light chainC [auth H]221Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SOG
Query on SOG

Download Ideal Coordinates CCD File 
D [auth A]octyl 1-thio-beta-D-glucopyranoside
C14 H28 O5 S
CGVLVOOFCGWBCS-RGDJUOJXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.838α = 90
b = 169.804β = 90
c = 130.417γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-04
    Type: Initial release
  • Version 1.1: 2012-01-18
    Changes: Database references, Structure summary
  • Version 1.2: 2012-01-25
    Changes: Database references
  • Version 1.3: 2012-02-01
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary