6BMH

Crystal structure of MHC-I like protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.298 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history. 

Literature

Differing roles of CD1d2 and CD1d1 proteins in type I natural killer T cell development and function.

Sundararaj, S., Zhang, J., Krovi, S.H., Bedel, R., Tuttle, K.D., Veerapen, N., Besra, G.S., Khandokar, Y., Praveena, T., Le Nours, J., Matsuda, J.L., Rossjohn, J., Gapin, L.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E1204-E1213

  • DOI: 10.1073/pnas.1716669115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • MHC class I-like CD1 molecules have evolved to present lipid-based antigens to T cells. Differences in the antigen-binding clefts of the CD1 family members determine the conformation and size of the lipids that are presented, although the factors tha ...

    MHC class I-like CD1 molecules have evolved to present lipid-based antigens to T cells. Differences in the antigen-binding clefts of the CD1 family members determine the conformation and size of the lipids that are presented, although the factors that shape CD1 diversity remain unclear. In mice, two homologous genes, CD1D1 and CD1D2, encode the CD1d protein, which is essential to the development and function of natural killer T (NKT) cells. However, it remains unclear whether both CD1d isoforms are equivalent in their antigen presentation capacity and functions. Here, we report that CD1d2 molecules are expressed in the thymus of some mouse strains, where they select functional type I NKT cells. Intriguingly, the T cell antigen receptor repertoire and phenotype of CD1d2-selected type I NKT cells in CD1D1-/- mice differed from CD1d1-selected type I NKT cells. The structures of CD1d2 in complex with endogenous lipids and a truncated acyl-chain analog of α-galactosylceramide revealed that its A'-pocket was restricted in size compared with CD1d1. Accordingly, CD1d2 molecules could not present glycolipid antigens with long acyl chains efficiently, favoring the presentation of short acyl chain antigens. These results indicate that the two CD1d molecules present different sets of self-antigen(s) in the mouse thymus, thereby impacting the development of invariant NKT cells.

    Organizational Affiliation: 

    Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d2
A, C, E, G
276Mus musculusMutation(s): 0 
Gene Names: Cd1d2 (Cd1.2)
Find proteins for P11610 (Mus musculus)
Go to UniProtKB:  P11610
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D, F, H
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F61
Query on F61
Download SDF File 
Download CCD File 
A, C, E, G
N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide
C35 H69 N O9
XAGHGLSSJDVTMX-NOUVZJLJSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, C, E, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.298 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 105.955α = 90.00
b = 74.229β = 102.94
c = 117.594γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Database references
  • Version 2.0: 2018-03-07
    Type: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary