3TVM

Structure of the mouse CD1d-SMC124-iNKT TCR complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report



Literature

Glycolipids that Elicit IFN-gama-Biased Responses from Natural Killer T Cells

Tyznik, A.J.Farber, E.Girardi, E.Birkholz, A.Li, Y.Chitale, S.So, R.Arora, P.Khurana, A.Wang, J.Porcelli, S.A.Zajonc, D.M.Kronenberg, M.Howell, A.R.

(2011) Chem Biol 18: 1620-1630

  • DOI: 10.1016/j.chembiol.2011.10.015
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Natural killer T (NKT) cells recognize glycolipids presented by CD1d. The first antigen described, α-galactosyl ceramide (αGalCer), is a potential anticancer agent whose activity depends upon IFN-γ secretion. We report two analogs of αGalCer based on ...

    Natural killer T (NKT) cells recognize glycolipids presented by CD1d. The first antigen described, α-galactosyl ceramide (αGalCer), is a potential anticancer agent whose activity depends upon IFN-γ secretion. We report two analogs of αGalCer based on a naturally occurring glycosphingolipid, plakoside A. These compounds induce enhanced IFN-γ that correlates with detergent-resistant binding to CD1d and an increased stability of the lipid-CD1d complexes on antigen-presenting cells. Structural analysis on one of the analogs indicates that it is more deeply bound inside the CD1d groove, suggesting tighter lipid-CD1d interactions. To our knowledge, this is the first example in which structural information provides an explanation for the increased lipid-CD1d stability, likely responsible for the Th1 bias. We provide insights into the mechanism of IFN-γ-inducing compounds, and because our compounds activate human NKT cells, they could have therapeutic utility.


    Organizational Affiliation

    Division of Developmental Immunology, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
A, E
285Mus musculusMutation(s): 1 
Gene Names: Cd1.1CD1dCd1d1
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
beta-2-microglobulin
B, F
99Mus musculusMutation(s): 1 
Gene Names: beta-2-microglobulinB2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Valpha14 (mouse variable domain, human constant domain)
C, G
209Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Valpha14 (mouse variable domain
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Vbeta8.2 (mouse variable domain, human constant domain)
D, H
241Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Vbeta8.2 (mouse variable domain
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
07P
Query on 07P

Download CCD File 
A, E
N-[(2S,3R)-10-[(1R,2R)-2-decylcyclopropyl]-1-(alpha-D-galactopyranosyloxy)-3-hydroxydecan-2-yl]hexacosanamide
C55 H107 N O8
BCHXWZQXEKOXKQ-IYKQKVLOSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUC
Query on FUC

Download CCD File 
A, E
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
E
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.97α = 90
b = 150.57β = 96.35
c = 101.96γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release