PDBsum entry 5efi

Immune system

PDB id: 5efi

Contents

Protein chains

263 a.a.

99 a.a.

16 a.a.

Ligands

NAG-NAG

NAG-NAG-BMA-MAN-MAN-FUC

NAG

CIT

PLM

OCA

Metals

_NA

Waters ×204

PDB id:

5efi

Name:

Immune system

Title:

Crystal structure of mouse cd1d in complex with the p99p lipopeptide

Structure:

Antigen-presenting glycoprotein cd1d1. Chain: a. Engineered: yes. Beta-2-microglobulin. Chain: b. Engineered: yes. P99p. Chain: c. Engineered: yes.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: cd1d1, cd1.1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: b2m. Synthetic: yes. Mus.

Resolution:

1.80Å R-factor: 0.220 R-free: 0.244

Authors:

E.Girardi,J.Wang,D.M.Zajonc

Key ref:

E.Girardi et al. (2016). Structure of an α-Helical Peptide and Lipopeptide Bound to the Nonclassical Major Histocompatibility Complex (MHC) Class I Molecule CD1d. J Biol Chem, 291, 10677-10683. PubMed id: 27006394 DOI: 10.1074/jbc.M115.702118

Date:

23-Oct-15 Release date: 30-Mar-16

Protein chain

P11609  (CD1D1_MOUSE) -  Antigen-presenting glycoprotein CD1d1 from Mus musculus

Seq: 336 a.a.

Struc: 263 a.a.

Protein chain

P01887  (B2MG_MOUSE) -  Beta-2-microglobulin from Mus musculus

Seq: 119 a.a.

Struc: 99 a.a.

Protein chain

No UniProt id for this chain

Struc: 16 a.a.

DOI no: 10.1074/jbc.M115.702118

J Biol Chem 291:10677-10683 (2016)

PubMed id: 27006394

Structure of an α-Helical Peptide and Lipopeptide Bound to the Nonclassical Major Histocompatibility Complex (MHC) Class I Molecule CD1d.

E.Girardi, J.Wang, D.M.Zajonc.

ABSTRACT

Mouse CD1d is a nonclassical MHC molecule able to present lipids and glycolipids to a specialized subset of T cells known as natural killer T cells. The antigens presented by CD1d have been shown to cover a broad range of chemical structures and to follow precise rules determining the potency of the antigen in the context of T cell activation. Together with lipids, initial reports suggested that CD1d can also bind and present hydrophobic peptides with (F/W)XX(I/L/M)XXW. However, the exact location of peptide binding and the molecular basis for the required motif are currently unknown. Here we present the crystal structure of the first peptide identified to bind CD1d, p99, and show that it binds in the antigen-binding groove of CD1d in a manner compatible with its presentation to T cell receptors. Interestingly, the peptide adopts an α-helical conformation, which orients the motif residues toward its deep binding groove, therefore explaining the molecular requirements for peptide binding. Moreover, we demonstrate that a lipopeptide version of the same peptide is able to bind CD1d in a similar conformation, identifying another class of molecules binding this antigen-presenting molecule.