4GBY | pdb_00004gby

The structure of the MFS (major facilitator superfamily) proton:xylose symporter XylE bound to D-xylose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.274 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 2.1 of the entry. See complete history


Literature

Crystal structure of a bacterial homologue of glucose transporters GLUT1-4.

Sun, L.Zeng, X.Yan, C.Sun, X.Gong, X.Rao, Y.Yan, N.

(2012) Nature 490: 361-366

  • DOI: https://doi.org/10.1038/nature11524
  • Primary Citation of Related Structures:  
    4GBY, 4GBZ, 4GC0

  • PubMed Abstract: 

    Glucose transporters are essential for metabolism of glucose in cells of diverse organisms from microbes to humans, exemplified by the disease-related human proteins GLUT1, 2, 3 and 4. Despite rigorous efforts, the structural information for GLUT1-4 or their homologues remains largely unknown. Here we report three related crystal structures of XylE, an Escherichia coli homologue of GLUT1-4, in complex with d-xylose, d-glucose and 6-bromo-6-deoxy-D-glucose, at resolutions of 2.8, 2.9 and 2.6 Å, respectively. The structure consists of a typical major facilitator superfamily fold of 12 transmembrane segments and a unique intracellular four-helix domain. XylE was captured in an outward-facing, partly occluded conformation. Most of the important amino acids responsible for recognition of D-xylose or d-glucose are invariant in GLUT1-4, suggesting functional and mechanistic conservations. Structure-based modelling of GLUT1-4 allows mapping and interpretation of disease-related mutations. The structural and biochemical information reported here constitutes an important framework for mechanistic understanding of glucose transporters and sugar porters in general.


  • Organizational Affiliation

    State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, Tsinghua University, Beijing 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-xylose-proton symporter491Escherichia coli K-12Mutation(s): 0 
Gene Names: xylEb4031JW3991
Membrane Entity: Yes 
UniProt
Find proteins for P0AGF4 (Escherichia coli (strain K12))
Explore P0AGF4 
Go to UniProtKB:  P0AGF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AGF4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.274 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.29α = 90
b = 95.29β = 90
c = 168.181γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXSphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BNGClick on this verticalbar to view detailsBest fitted XYPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references, Structure summary