6QSK

Crystal structure of a nucleotide sugar transporter with bound nucleotide monophosphate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for substrate specificity and regulation of nucleotide sugar transporters in the lipid bilayer.

Parker, J.L.Corey, R.A.Stansfeld, P.J.Newstead, S.

(2019) Nat Commun 10: 4657-4657

  • DOI: https://doi.org/10.1038/s41467-019-12673-w
  • Primary Citation of Related Structures:  
    6QSK

  • PubMed Abstract: 

    Nucleotide sugars are the activated form of monosaccharides used by glycosyltransferases during glycosylation. In eukaryotes the SLC35 family of solute carriers are responsible for their selective uptake into the Endoplasmic Reticulum or Golgi apparatus. The structure of the yeast GDP-mannose transporter, Vrg4, revealed a requirement for short chain lipids and a marked difference in transport rate between the nucleotide sugar and nucleoside monophosphate, suggesting a complex network of regulatory elements control transport into these organelles. Here we report the crystal structure of the GMP bound complex of Vrg4, revealing the molecular basis for GMP recognition and transport. Molecular dynamics, combined with biochemical analysis, reveal a lipid mediated dimer interface and mechanism for coordinating structural rearrangements during transport. Together these results provide further insight into how SLC35 family transporters function within the secretory pathway and sheds light onto the role that membrane lipids play in regulating transport across the membrane.


  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. joanne.parker@bioch.ox.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GDP-mannose transporter 1
A, B, C, D, E
A, B, C, D, E, F, G, H
337Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VRG4GOG5LDB3MCD3VAN2VIG4YGL225W
Membrane Entity: Yes 
UniProt
Find proteins for P40107 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40107 
Go to UniProtKB:  P40107
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40107
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.705α = 89.93
b = 102.716β = 90.08
c = 181.253γ = 90.19
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom102890/Z/13/A

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description