3TIJ

Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.436 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4A

Johnson, Z.L.Cheong, C.G.Lee, S.Y.

(2012) Nature 483: 489-493

  • DOI: 10.1038/nature10882

  • PubMed Abstract: 
  • Nucleosides are required for DNA and RNA synthesis, and the nucleoside adenosine has a function in a variety of signalling processes. Transport of nucleosides across cell membranes provides the major source of nucleosides in many cell types and is al ...

    Nucleosides are required for DNA and RNA synthesis, and the nucleoside adenosine has a function in a variety of signalling processes. Transport of nucleosides across cell membranes provides the major source of nucleosides in many cell types and is also responsible for the termination of adenosine signalling. As a result of their hydrophilic nature, nucleosides require a specialized class of integral membrane proteins, known as nucleoside transporters (NTs), for specific transport across cell membranes. In addition to nucleosides, NTs are important determinants for the transport of nucleoside-derived drugs across cell membranes. A wide range of nucleoside-derived drugs, including anticancer drugs (such as Ara-C and gemcitabine) and antiviral drugs (such as zidovudine and ribavirin), have been shown to depend, at least in part, on NTs for transport across cell membranes. Concentrative nucleoside transporters, members of the solute carrier transporter superfamily SLC28, use an ion gradient in the active transport of both nucleosides and nucleoside-derived drugs against their chemical gradients. The structural basis for selective ion-coupled nucleoside transport by concentrative nucleoside transporters is unknown. Here we present the crystal structure of a concentrative nucleoside transporter from Vibrio cholerae in complex with uridine at 2.4 Å. Our functional data show that, like its human orthologues, the transporter uses a sodium-ion gradient for nucleoside transport. The structure reveals the overall architecture of this class of transporter, unravels the molecular determinants for nucleoside and sodium binding, and provides a framework for understanding the mechanism of nucleoside and nucleoside drug transport across cell membranes.


    Organizational Affiliation

    Department of Biochemistry and Ion Channel Research Unit, Duke University Medical Center, 2 Genome Court, Durham, North Carolina 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NupC family protein
A
424Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)N/A
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Solute Carrier (SLC) Transporter Superfamily
Protein: 
Concentrative nucleoside transporter (CNT) in complex with uridine
Find proteins for Q9KPL5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KPL5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DMU
Query on DMU

Download SDF File 
Download CCD File 
A
DECYL-BETA-D-MALTOPYRANOSIDE
DECYLMALTOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
URI
Query on URI

Download SDF File 
Download CCD File 
A
URIDINE
C9 H12 N2 O6
DRTQHJPVMGBUCF-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.436 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 119.717α = 90.00
b = 119.717β = 90.00
c = 83.136γ = 120.00
Software Package:
Software NamePurpose
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references