PDBsum entry 1qo3

Receptor/immune system

PDB id: 1qo3

Contents

Protein chains

274 a.a. *

100 a.a. *

128 a.a. *

121 a.a. *

Ligands

ARG-GLY-PRO-GLY-ARG-ALA-PHE-VAL-THR-ILE

EDO ×3

Waters ×352

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of a lectin-Like natural killer cell receptor bound to its mhc class i ligand.

Authors

J.Tormo, K.Natarajan, D.H.Margulies, R.A.Mariuzza.

Ref.

Nature, 1999, 402, 623-631. [DOI no: 10.1038/45170]

PubMed id

10604468

Abstract

Natural killer (NK) cell function is regulated by NK receptors that interact with MHC class I (MHC-I) molecules on target cells. The murine NK receptor Ly49A inhibits NK cell activity by interacting with H-2D(d) through its C-type-lectin-like NK receptor domain. Here we report the crystal structure of the complex between the Ly49A NK receptor domain and unglycosylated H-2D(d). The Ly49A dimer interacts extensively with two H-2D(d) molecules at distinct sites. At one interface, a single Ly49A subunit contacts one side of the MHC-I peptide-binding platform, presenting an open cavity towards the conserved glycosylation site on the H-2D(d) alpha2 domain. At a second, larger interface, the Ly49A dimer binds in a region overlapping the CD8-binding site. The smaller interface probably represents the interaction between Ly49A on the NK cell and MHC-I on the target cell, whereas the larger one suggests an interaction between Ly49A and MHC-I on the NK cell itself. Both Ly49A binding sites on MHC-I are spatially distinct from that of the T-cell receptor.

Figure 1.
Figure 1 Structure of the Ly49A/H-2D^d complex and the interaction sites. a, Stereo diagram of the complex and crystal packing interactions. View shows the asymmetric interaction between an Ly49A dimer and two H-2D^d molecules related by the crystal symmetry. The H-2D^d heavy chain is yellow, [2]m is grey, and the two Ly49A subunits, Ly49A-1 and Ly49A-2, are cyan and blue, respectively, whereas the viral peptide is shown in orange ball-and-stick representation. The two interaction surfaces, site 1 and site 2, are indicated by a red circle and a black rectangle, respectively. b, c, Detailed view of site 1 showing the interactions using a common orientation based on the 'standard' view for the MHC-I molecule. c, Close up of the interactions at site 1. The view has been rotated around the horizontal relative to b and depicts the region highlighted by a box. d, e, As in b, c but for site 2. The two domains of the MHC-I peptide-binding platform are shown in cream ( 1) and dark yellow ( 2). Hydrogen bonds between Ly49A and H-2D^d are depicted as broken lines. All figures were drawn using programs BOBSCRIPT49 and Raster3D^50.

Figure 5.
Figure 5 The putative carbohydrate-binding pocket at the Ly49A/H-2D^d interface. A close-up of the complex interface at site 1 is shown, centred at the open cavity around N176, a conserved glycosylation site in rodent MHC-I molecules. The orientation and the polypeptide chain representation are as in Fig. 1b. Two proximal carbohydrates, a GlcNAc and a fucose residue, have been modelled on the basis of crystal structures of MHC-I molecules deposited in the Protein Data Bank. The carbohydrate residues (pink) and surrounding amino-acid side chains (cyan for Ly49A and yellow for H-2D^d) are shown in ball-and-stick representation; the branching fucose residue could fit well into the deep open pocket. The red arrow indicates position 4 in the GluNAc residue where the rest of the oligosaccharide is attached, and which can establish further interactions along the flat surface of the Ly49A dimer (Fig. 1b).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 402, 623-631) copyright 1999.

Secondary reference #1

Title

Interaction of the nk cell inhibitory receptor ly49a with h-2dd: identification of a site distinct from the tcr site.

Authors

K.Natarajan, L.F.Boyd, P.Schuck, W.M.Yokoyama, D.Eliat, D.H.Margulies.

Ref.

Immunity, 1999, 11, 591-601. [DOI no: 10.1016/S1074-7613(00)80134-X]

PubMed id

10591184

Figure 2.
Figure 2. Anti-Ly49A Monoclonal Antibodies Specifically Bind to Ly49A EC and Ly49A NKD-LPurified preparations of the three indicated molecules were immobilized to a CM-5 chip and analyzed for binding to the indicated mAbs by SPR using the BIACore 2000 as described in the Experimental Procedures. Solution phase analytes (mAbs) were injected at T = 83 s. Dissociation washout was initiated at T = 365 s. To evaluate the potential for deterioration of the coupled surfaces with successive cycles of binding and regeneration, mAb A1 was used in the first (solid circle) and last (open square) runs.

Figure 5.
Figure 5. Staining of Splenocytes with Biotinylated Ly49A EC(A) Splenocytes (1 × 10^6) from C57Bl/6 (H-2^b), BALB/c (H-2^d), and C3H/HeJ (H-2^k) mice were incubated with biotinylated Ly49A EC and PE-SA and analyzed by flow cytometry as described in the Experimental Procedures. Background staining with PE-SA alone was identical for all three strains. Staining of splenocytes from BALB/c (B), C57BL/6 (C), and β2m^−/− (D) mice was performed as above, using a lower concentration of the bio-Ly49A (dark lines). Competition with unlabeled Ly49A (dotted lines) was carried out (see the Experimental Procedures).

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #2

Title

Three-Dimensional structure of h-2dd complexed with an immunodominant peptide from human immunodeficiency virus envelope glycoprotein 120.

Authors

H.Li, K.Natarajan, E.L.Malchiodi, D.H.Margulies, R.A.Mariuzza.

Ref.

J Mol Biol, 1998, 283, 179-191. [DOI no: 10.1006/jmbi.1998.2091]

PubMed id

9761682

Figure 1.
Figure 1. Ribbon diagram of the H-2D^d/P18-I10 complex. The a1, a2, a3 and b[2]m domains are labeled. All Figures were generated by MOLSCRIPT [Kraulis 1991] and Raster3D [Bacon and Anderson 1988 and Merritt and Bacon 1997] if not specified.

Figure 6.
Figure 6. Location of H-2D^dresidues implicated in binding the NK inhibitory receptor Ly-49A. The P18-I10 peptide is yellow; the a1 and a2 domains of D^dare labeled. In pink are residues of in the a1 domain and N-terminal portion of the a2 domain of D^dthat differ in D^b. In blue are D^dresidues that have different side-chain conformations in Kb, Ldor D^b. In red is the N-terminal part of the a2 domain of D^d(residues 90 to 107).

The above figures are reproduced from the cited reference with permission from Elsevier