3DH4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    3DH4

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/glucose cotransporterABCD530Vibrio parahaemolyticusMutation(s): 0 
Gene Names: sglT
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Solute Sodium Symporter (SSS) Family
Protein: 
vSGLT Sodium Galactose Transporter
Find proteins for P96169 (Vibrio parahaemolyticus)
Explore P96169 
Go to UniProtKB:  P96169
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download CCD File 
A, B, C, D
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
ER3
Query on ER3

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

Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.28α = 109.7
b = 109.21β = 92.02
c = 127.58γ = 102.11
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary