6E9N

E. coli D-galactonate:proton symporter in the inward open form

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

  • Deposited: 2018-08-01 Released: 2019-05-22 
  • Deposition Author(s): Leano, J.B., Edwards, R.H., Stroud, R.M.
  • Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 


Literature

Structures suggest a mechanism for energy coupling by a family of organic anion transporters.

Leano, J.B., Batarni, S., Eriksen, J., Juge, N., Pak, J.E., Kimura-Someya, T., Robles-Colmenares, Y., Moriyama, Y., Stroud, R.M., Edwards, R.H.

(2019) PLoS Biol 17: e3000260-e3000260

  • DOI: https://doi.org/10.1371/journal.pbio.3000260
  • Primary Citation of Related Structures:  
    6E9N, 6E9O

  • PubMed Abstract: 

    • Members of the solute carrier 17 (SLC17) family use divergent mechanisms to concentrate organic anions. Membrane potential drives uptake of the principal excitatory neurotransmitter glutamate into synaptic vesicles, whereas closely related proteins use proton cotransport to drive efflux from the lysosome ...

    Members of the solute carrier 17 (SLC17) family use divergent mechanisms to concentrate organic anions. Membrane potential drives uptake of the principal excitatory neurotransmitter glutamate into synaptic vesicles, whereas closely related proteins use proton cotransport to drive efflux from the lysosome. To delineate the divergent features of ionic coupling by the SLC17 family, we determined the structure of Escherichia coli D-galactonate/H+ symporter D-galactonate transporter (DgoT) in 2 states: one open to the cytoplasmic side and the other open to the periplasmic side with substrate bound. The structures suggest a mechanism that couples H+ flux to substrate recognition. A transition in the role of H+ from flux coupling to allostery may confer regulation by trafficking to and from the plasma membrane.

    Organizational Affiliation: 

    Departments of Neurology and Physiology, University of California San Francisco School of Medicine, San Francisco, California, United States of America.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-galactonate transportA, B460Escherichia coliMutation(s): 0 
Gene Names: 
Membrane Entity: Yes 
UniProt
Find proteins for J7QAK3 (Escherichia coli)
Explore J7QAK3 
Go to UniProtKB:  J7QAK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7QAK3
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.7α = 90
b = 107.63β = 108.32
c = 103.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesMH50712
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM24485
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS089713
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM024485-37S1

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary