6WTX

Structure of VcINDY in complex with terephthalate

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Vibrio cholerae
  • Expression System: Escherichia coli
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTMMemProtMDmpstruc

  • Deposited: 2020-05-04 Released: 2020-09-16 
  • Deposition Author(s): Sauer, D.B., Marden, J.J., Wang, D.N.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.92 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.291 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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

    Department of 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 symporterA [auth C],
B [auth D],
C [auth A],
D [auth B]
449Vibrio choleraeMutation(s): 0 
Gene Names: VC0395_0108GG844_00510
Membrane Entity: Yes 
UniProt
Find proteins for Q9KNE0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KNE0 
Go to UniProtKB:  Q9KNE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KNE0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UB7 (Subject of Investigation/LOI)
Query on UB7

Download Ideal Coordinates CCD File 
E [auth C],
H [auth D],
M [auth A],
N [auth B]
terephthalic acid
C8 H6 O4
KKEYFWRCBNTPAC-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth C]
G [auth C]
I [auth D]
J [auth D]
K [auth A]
F [auth C],
G [auth C],
I [auth D],
J [auth D],
K [auth A],
L [auth A],
O [auth B],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.92 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.291 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.458α = 90
b = 103.062β = 95.848
c = 174.447γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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

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