6Z6Y

Galectin-8 N-terminal domain in complex with a sulfatide mimicking a sphingolipid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Probing sulfatide-tissue lectin recognition with functionalized glycodendrimersomes.

Murphy, P.V.Romero, A.Xiao, Q.Ludwig, A.K.Jogula, S.Shilova, N.V.Singh, T.Gabba, A.Javed, B.Zhang, D.Medrano, F.J.Kaltner, H.Kopitz, J.Bovin, N.V.Wu, A.M.Klein, M.L.Percec, V.Gabius, H.J.

(2021) iScience 24: 101919-101919

  • DOI: https://doi.org/10.1016/j.isci.2020.101919
  • Primary Citation of Related Structures:  
    6Z6Y

  • PubMed Abstract: 

    The small 3- O -sulfated galactose head group of sulfatides, an abundant glycosphingolipid class, poses the (sphinx-like) riddle on involvement of glycan bridging by tissue lectins (sugar code). First, synthesis of head group derivatives for functionalization of amphiphilic dendrimers is performed. Aggregation of resulting (biomimetic) vesicles, alone or in combination with lactose, demonstrates bridging by a tissue lectin (galectin-4). Physiologically, this can stabilize glycolipid-rich microdomains (rafts) and associate sulfatide-rich regions with specific glycoproteins. Further testing documents importance of heterobivalency and linker length. Structurally, sulfatide recognition by galectin-8 is shown to involve sphingosine's OH group as substitute for the 3'-hydroxyl of glucose of lactose. These discoveries underscore functionality of this small determinant on biomembranes intracellularly and on the cell surface. Moreover, they provide a role model to examine counterreceptor capacity of more complex glycans of glycosphingolipids and to start their bottom-up glycotope surface programming.


  • Organizational Affiliation

    CÚRAM - SFI Research Centre for Medical Devices and the School of Chemistry, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-8156Homo sapiensMutation(s): 0 
Gene Names: LGALS8
UniProt & NIH Common Fund Data Resources
Find proteins for O00214 (Homo sapiens)
Explore O00214 
Go to UniProtKB:  O00214
PHAROS:  O00214
GTEx:  ENSG00000116977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00214
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L4L (Subject of Investigation/LOI)
Query on L4L

Download Ideal Coordinates CCD File 
B [auth A][(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{S})-2-acetamido-3-oxidanylidene-pent-4-enoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl] hydrogen sulfate
C13 H21 N O11 S
XMURRHZYXOXPBZ-FJUAUIJYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
I [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.64α = 90
b = 40.066β = 99.803
c = 40.701γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2016-77835-R

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 2.0: 2022-07-20
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Refinement description