6WTW

Structure of LaINDY crystallized in the presence of alpha-ketoglutarate and malate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the reaction cycle of DASS dicarboxylate transporters.

Sauer, D.B.Trebesch, N.Marden, J.J.Cocco, N.Song, J.Koide, A.Koide, S.Tajkhorshid, E.Wang, D.N.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.61350
  • Primary Citation of Related Structures:  
    6WTW, 6WTX, 6WU1, 6WU2, 6WU3, 6WU4, 6WW5

  • PubMed Abstract: 

    Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the cell by the divalent anion sodium symporter (DASS) family of plasma membrane transporters, which contains both cotransporters and exchangers. While DASS proteins transport substrates via an elevator mechanism, to date structures are only available for a single DASS cotransporter protein in a substrate-bound, inward-facing state. We report multiple cryo-EM and X-ray structures in four different states, including three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter and an exchanger. Comparison of these outward- and inward-facing structures reveal how the transport domain translates and rotates within the framework of the scaffold domain through the transport cycle. Additionally, we propose that DASS transporters ensure substrate coupling by a charge-compensation mechanism, and by structural changes upon substrate release.


  • Organizational Affiliation

    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DASS family sodium-coupled anion symporter
A, B
491Lactobacillus acidophilusMutation(s): 0 
Gene Names: D7H66_01865
Membrane Entity: Yes 
UniProt
Find proteins for Q5FKK5 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM))
Explore Q5FKK5 
Go to UniProtKB:  Q5FKK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5FKK5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.328α = 90
b = 76.609β = 90.485
c = 96.946γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS108151
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM121994
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK099023
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description