3DH4

Crystal Structure of Sodium/Sugar symporter with bound Galactose from vibrio parahaemolyticus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport.

Faham, S.Watanabe, A.Besserer, G.M.Cascio, D.Specht, A.Hirayama, B.A.Wright, E.M.Abramson, J.

(2008) Science 321: 810-814

  • DOI: 10.1126/science.1160406

  • PubMed Abstract: 
  • Membrane transporters that use energy stored in sodium gradients to drive nutrients into cells constitute a major class of proteins. We report the crystal structure of a member of the solute sodium symporters (SSS), the Vibrio parahaemolyticus sodium ...

    Membrane transporters that use energy stored in sodium gradients to drive nutrients into cells constitute a major class of proteins. We report the crystal structure of a member of the solute sodium symporters (SSS), the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT). The approximately 3.0 angstrom structure contains 14 transmembrane (TM) helices in an inward-facing conformation with a core structure of inverted repeats of 5 TM helices (TM2 to TM6 and TM7 to TM11). Galactose is bound in the center of the core, occluded from the outside solutions by hydrophobic residues. Surprisingly, the architecture of the core is similar to that of the leucine transporter (LeuT) from a different gene family. Modeling the outward-facing conformation based on the LeuT structure, in conjunction with biophysical data, provides insight into structural rearrangements for active transport.


    Organizational Affiliation

    Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1751, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium/glucose cotransporter
A, B, C, D
530Vibrio parahaemolyticusMutation(s): 0 
Gene Names: sglT
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Solute Sodium Symporter (SSS) Family
Protein: 
vSGLT Sodium Galactose Transporter
Find proteins for P96169 (Vibrio parahaemolyticus)
Go to UniProtKB:  P96169
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ER3
Query on ER3

Download SDF File 
Download CCD File 
A, D
ERBIUM (III) ION
Er
JHFPQYFEJICGKC-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B, C, D
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B, C, D
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.270 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 83.280α = 109.70
b = 109.210β = 92.02
c = 127.580γ = 102.11
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description