4ZAK

Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.824 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Novel Glycolipid Antigen for NKT Cells That Preferentially Induces IFN-gamma Production.

Birkholz, A.M.Girardi, E.Wingender, G.Khurana, A.Wang, J.Zhao, M.Zahner, S.Illarionov, P.A.Wen, X.Li, M.Yuan, W.Porcelli, S.A.Besra, G.S.Zajonc, D.M.Kronenberg, M.

(2015) J Immunol. 195: 924-933

  • DOI: 10.4049/jimmunol.1500070

  • PubMed Abstract: 
  • In this article, we characterize a novel Ag for invariant NKT (iNKT) cells capable of producing an especially robust Th1 response. This glycosphingolipid, DB06-1, is similar in chemical structure to the well-studied α-galactosylceramide (αGalCer), wi ...

    In this article, we characterize a novel Ag for invariant NKT (iNKT) cells capable of producing an especially robust Th1 response. This glycosphingolipid, DB06-1, is similar in chemical structure to the well-studied α-galactosylceramide (αGalCer), with the only change being a single atom: the substitution of a carbonyl oxygen with a sulfur atom. Although DB06-1 is not a more effective Ag in vitro, the small chemical change has a marked impact on the ability of this lipid Ag to stimulate iNKT cells in vivo, with increased IFN-γ production at 24 h compared with αGalCer, increased IL-12, and increased activation of NK cells to produce IFN-γ. These changes are correlated with an enhanced ability of DB06-1 to load in the CD1d molecules expressed by dendritic cells in vivo. Moreover, structural studies suggest a tighter fit into the CD1d binding groove by DB06-1 compared with αGalCer. Surprisingly, when iNKT cells previously exposed to DB06-1 are restimulated weeks later, they have greatly increased IL-10 production. Therefore, our data are consistent with a model whereby augmented and or prolonged presentation of a glycolipid Ag leads to increased activation of NK cells and a Th1-skewed immune response, which may result, in part, from enhanced loading into CD1d. Furthermore, our data suggest that strong antigenic stimulation in vivo may lead to the expansion of IL-10-producing iNKT cells, which could counteract the benefits of increased early IFN-γ production.


    Organizational Affiliation

    Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92037;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
A
285Mus musculusMutation(s): 0 
Gene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein Trav11,Va14Ja18/Vb8.2,Human nkt tcr alpha chain
C
209Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trav11 (Trav11d), Traj18, B2M
Find proteins for A0A0B4J1J9 (Mus musculus)
Go to UniProtKB:  A0A0B4J1J9
Find proteins for A0A0G2JG46 (Mus musculus)
Go to UniProtKB:  A0A0G2JG46
Find proteins for K7N5M3 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  K7N5M3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C region,Protein Trbc2,T-cell receptor beta-2 chain C region
D
241Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 2 
Gene Names: TRBC2 (TCRBC2),
Find proteins for A2NTY6 (Mus musculus)
Go to UniProtKB:  A2NTY6
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Find proteins for A0N8J3 (Mus musculus)
Go to UniProtKB:  A0N8J3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4LX
Query on 4LX

Download SDF File 
Download CCD File 
A
N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanethioamide
C50 H99 N O8 S
MSKBSPRYFRAUPB-BYSUZVQFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.824 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 78.921α = 90.00
b = 190.544β = 90.00
c = 150.760γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
Blu-Icedata collection
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI074952

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-29
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Derived calculations, Source and taxonomy