ISDA

Deposition Date 2009-05-07

Release Date 2009-07-28

Last Version Date 2024-10-30

Entry Detail

PDB ID:

3HE6

Keywords:

IMMUNE SYSTEM

Title:

Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta8.2 NKT TCR

Biological Source:

Source Organism:

Mus musculus (Taxon ID: 10090)

Host Organism:

Trichoplusia ni

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.90 Å

R-Value Free:

0.29

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Antigen-presenting glycoprotein CD1d1
Gene (Uniprot):Cd1d1
Chain IDs:A
Chain Length:302
Number of Molecules:1
Biological Source:Mus musculus

UniProt ID:P11609 Pfam ID:PF16497, PF07654

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Beta-2-microglobulin
Gene (Uniprot):B2m
Chain IDs:B
Chain Length:99
Number of Molecules:1
Biological Source:Mus musculus

UniProt ID:P01887 Pfam ID:PF07654

Polymer Type:polypeptide(L)
Molecule:Valpha14(mouse variable domain, human constant domain)
Chain IDs:C
Chain Length:207
Number of Molecules:1
Biological Source:Mus musculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Vbeta8.2(mouse variable domain, human constant domain)
Chain IDs:D
Chain Length:244
Number of Molecules:1
Biological Source:Mus musculus

UniProt ID:P01850 Pfam ID:PF07654

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
ASN	A	ASN	GLYCOSYLATION SITE

Ligand Molecules

AGH

NAG

Primary Citation

Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors

Pellicci, D.G, Patel, O, Kjer-Nielsen, L, Pang, S.S, Sullivan, L.C, Kyparissoudis, K, Brooks, A.G, Reid, H.H, Gras, S, Lucet, I.S, Koh, R, Smyth, M.J, Mallevaey, T, Matsuda, J.L, Gapin, L, McCluskey, J, Godfrey, D.I, Rossjohn, J.Show

Immunity 31 47 59 (2009)

PMID: 19592275 DOI: 10.1016/j.immuni.2009.04.018

Abstact

The semi-invariant natural killer T cell receptor (NKT TCR) recognizes CD1d-lipid antigens. Although the TCR alpha chain is typically invariant, the beta chain expression is more diverse, where three V beta chains are commonly expressed in mice. We report the structures of V alpha 14-V beta 8.2 and V alpha 14-V beta 7 NKT TCRs in complex with CD1d-alpha-galactosylceramide (alpha-GalCer) and the 2.5 A structure of the human NKT TCR-CD1d-alpha-GalCer complex. Both V beta 8.2 and V beta 7 NKT TCRs and the human NKT TCR ligated CD1d-alpha-GalCer in a similar manner, highlighting the evolutionarily conserved interaction. However, differences within the V beta domains of the V beta 8.2 and V beta 7 NKT TCR-CD1d complexes resulted in altered TCR beta-CD1d-mediated contacts and modulated recognition mediated by the invariant alpha chain. Mutagenesis studies revealed the differing contributions of V beta 8.2 and V beta 7 residues within the CDR2 beta loop in mediating contacts with CD1d. Collectively we provide a structural basis for the differential NKT TCR V beta usage in NKT cells.

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Primary Citation of related structures