7T9G

Structure of VcINDY-Na+

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

  • Deposited: 2021-12-19 Released: 2022-05-25 
  • Deposition Author(s): Sauer, D.B., Marden, J.J., Song, J.M., 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), American Cancer Society, Department of Defense (DOD, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of ion - substrate coupling in the Na + -dependent dicarboxylate transporter VcINDY.

Sauer, D.B.Marden, J.J.Sudar, J.C.Song, J.Mulligan, C.Wang, D.N.

(2022) Nat Commun 13: 2644-2644

  • DOI: https://doi.org/10.1038/s41467-022-30406-4
  • Primary Citation of Related Structures:  
    7T9F, 7T9G

  • PubMed Abstract: 

    The Na + -dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na + gradient to power substrate transport is well established for VcINDY, the structural basis of this coupling between sodium and substrate binding is not currently understood. Here, using a combination of cryo-EM structure determination, succinate binding and site-directed cysteine alkylation assays, we demonstrate that the VcINDY protein couples sodium- and substrate-binding via a previously unseen cooperative mechanism by conformational selection. In the absence of sodium, substrate binding is abolished, with the succinate binding regions exhibiting increased flexibility, including HP in b, TM10b and the substrate clamshell motifs. Upon sodium binding, these regions become structurally ordered and create a proper binding site for the substrate. Taken together, these results provide strong evidence that VcINDY's conformational selection mechanism is a result of the sodium-dependent formation of the substrate binding site.


  • Organizational Affiliation

    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DASS family sodium-coupled anion symporterA,
B [auth Y]
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



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
American Cancer SocietyUnited States129844-PF-17-135-01-TBE
Department of Defense (DOD, United States)United StatesW81XWH-16-1-0153

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Refinement description