5OGK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural basis of nucleotide sugar transport across the Golgi membrane.

Parker, J.L.Newstead, S.

(2017) Nature 551: 521-524

  • DOI: https://doi.org/10.1038/nature24464
  • Primary Citation of Related Structures:  
    5OGE, 5OGK

  • PubMed Abstract: 

    Glycosylation is a fundamental cellular process that, in eukaryotes, occurs in the lumen of both the Golgi apparatus and the endoplasmic reticulum. Nucleotide sugar transporters (NSTs) are an essential component of the glycosylation pathway, providing the diverse range of substrates required for the glycosyltransferases. NSTs are linked to several developmental and immune disorders in humans, and in pathogenic microbes they have an important role in virulence. How NSTs recognize and transport activated monosaccharides, however, is currently unclear. Here we present the crystal structure of an NST, the GDP-mannose transporter Vrg4, in both the substrate-free and the bound states. A hitherto unobserved requirement of short-chain lipids in activating the transporter supports a model for regulation within the highly dynamic membranes of the Golgi apparatus. Our results provide a structural basis for understanding nucleotide sugar recognition, and provide insights into the transport and regulatory mechanism of this family of intracellular transporters.


  • Organizational Affiliation

    1Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDD
Query on GDD

Download Ideal Coordinates CCD File 
I [auth A],
N [auth D],
P [auth E]
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
C16 H25 N5 O16 P2
MVMSCBBUIHUTGJ-GDJBGNAASA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth C]
M [auth C]
O [auth D]
J [auth A],
K [auth A],
L [auth C],
M [auth C],
O [auth D],
Q [auth E],
R [auth G],
S [auth G]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.319α = 89.86
b = 101.694β = 90.07
c = 180.192γ = 90.11
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2017-12-06
    Changes: Database references
  • Version 1.3: 2018-10-03
    Changes: Data collection
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description