4F7C

Crystal structure of bovine CD1d with bound C12-di-sulfatide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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This is version 2.1 of the entry. See complete history


Literature

Crystal Structures of Bovine CD1d Reveal Altered αGalCer Presentation and a Restricted A' Pocket Unable to Bind Long-Chain Glycolipids.

Wang, J.Guillaume, J.Pauwels, N.Van Calenbergh, S.Van Rhijn, I.Zajonc, D.M.

(2012) PLoS One 7: e47989-e47989

  • DOI: https://doi.org/10.1371/journal.pone.0047989
  • Primary Citation of Related Structures:  
    4F7C, 4F7E

  • PubMed Abstract: 

    NKT cells play important roles in immune surveillance. They rapidly respond to pathogens by detecting microbial glycolipids when presented by the non-classical MHC I homolog CD1d. Previously, ruminants were considered to lack NKT cells due to the lack of a functional CD1D gene. However, recent data suggest that cattle express CD1d with unknown function. In an attempt to characterize the function of bovine CD1d, we assessed the lipid binding properties of recombinant Bos taurus CD1d (boCD1d) in vitro. BoCD1d is able to bind glycosphingolipids (GSLs) with fatty acid chain lengths of C₁₈, while GSLs with fatty acids of C₂₄ do not bind. Crystal structures of boCD1d bound to a short-chain C₁₂-di-sulfatide antigen, as well as short-chain C₁₆-αGalCer revealed that the Á pocket of boCD1d is restricted in size compared to that of both mouse and human CD1d, explaining the inability of long chain GSL's to bind to boCD1d. Moreover, while di-sulfatide is presented similarly compared to the presentation of sulfatide by mouse CD1d, αGalCer is presented differently at the cell surface, due to an amino acid Asp151Asn substitution that results in loss of intimate contacts between the αGalCer headgroup and CD1d. The altered αGalCer presentation by boCD1d also explains its lack of cross-activation of mouse iNKT cells and raises the interesting question of the nature and function of bovine lipid-reactive T cells.


  • Organizational Affiliation

    Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CD1D antigen, d polypeptide
A, C
283Bos taurusMutation(s): 0 
Gene Names: CD1D
UniProt
Find proteins for A1L565 (Bos taurus)
Explore A1L565 
Go to UniProtKB:  A1L565
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1L565
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, D
98Bos taurusMutation(s): 0 
Gene Names: B2M
UniProt
Find proteins for P01888 (Bos taurus)
Explore P01888 
Go to UniProtKB:  P01888
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01888
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, G
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G31886NL
GlyCosmos:  G31886NL
GlyGen:  G31886NL
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0SG
Query on 0SG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth C]
N-{(2S,3R,4E)-1-[(3,6-di-O-sulfo-beta-D-galactopyranosyl)oxy]-3-hydroxyoctadec-4-en-2-yl}dodecanamide
C36 H69 N O14 S2
JBJSVLZKWGLXMO-AZNTWQPMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.553α = 90
b = 168.553β = 90
c = 41.525γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary