4US3

Crystal Structure of the bacterial NSS member MhsT in an Occluded Inward-Facing State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.234 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LMUClick on this verticalbar to view detailsBest fitted BNGClick on this verticalbar to view detailsBest fitted TRPClick on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

A Mechanism for Intracellular Release of Na+ by Neurotransmitter/Sodium Symporters

Malinauskaite, L.Quick, M.Reinhard, L.Lyons, J.A.Yano, H.Javitch, J.A.Nissen, P.

(2014) Nat Struct Mol Biol 21: 1006

  • DOI: https://doi.org/10.1038/nsmb.2894
  • Primary Citation of Related Structures:  
    4US3, 4US4

  • PubMed Abstract: 

    Neurotransmitter/sodium symporters (NSSs) terminate synaptic signal transmission by Na+-dependent reuptake of released neurotransmitters. Key conformational states have been reported for the bacterial homolog LeuT and an inhibitor-bound Drosophila dopamine transporter. However, a coherent mechanism of Na+-driven transport has not been described. Here, we present two crystal structures of MhsT, an NSS member from Bacillus halodurans, in occluded inward-facing states with bound Na+ ions and L-tryptophan, providing insight into the cytoplasmic release of Na+. The switch from outward- to inward-oriented states is centered on the partial unwinding of transmembrane helix 5, facilitated by a conserved GlyX9Pro motif that opens an intracellular pathway for water to access the Na2 site. We propose a mechanism, based on our structural and functional findings, in which solvation through the TM5 pathway facilitates Na+ release from Na2 and the transition to an inward-open state.


  • Organizational Affiliation

    1] Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark. [2] Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRANSPORTER455Halalkalibacterium halodurans C-125Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9KDT3 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Explore Q9KDT3 
Go to UniProtKB:  Q9KDT3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KDT3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMU
Query on LMU

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
BNG
Query on BNG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
N [auth A]
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
TRP
Query on TRP

Download Ideal Coordinates CCD File 
B [auth A]TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-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: 2.10 Å
  • R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.28α = 90
b = 49.89β = 96.76
c = 110.05γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LMUClick on this verticalbar to view detailsBest fitted BNGClick on this verticalbar to view detailsBest fitted TRPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2014-10-15
    Changes: Database references
  • Version 1.3: 2014-11-19
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary