PDBsum entry 1g0x

Immune system

PDB id: 1g0x

Contents

Protein chain

192 a.a. *

Waters ×245

* Residue conservation analysis

PDB id:

1g0x

Name:

Immune system

Title:

Crystal structure of the ligand binding domain of lir-1 (ilt2)

Structure:

Leucocyte immunoglobulin-like receptor-1. Chain: a. Fragment: d1d2 ligand binding domain. Synonym: leukocyte inhibitory receptor-1. Leukocyte immunoglobulin- like receptor, subfamily b (with tm and itim domains), member 1. Leukocyte immunoglobulin-like receptor 1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.214 R-free: 0.244

Authors:

T.L.Chapman,A.P.Heikema,A.P.West Jr.,P.J.Bjorkman

Key ref:

T.L.Chapman et al. (2000). Crystal structure and ligand binding properties of the D1D2 region of the inhibitory receptor LIR-1 (ILT2). Immunity, 13, 727-736. PubMed id: 11114384 DOI: 10.1016/S1074-7613(00)00071-6

Date:

09-Oct-00 Release date: 17-Jan-01

Protein chain

Q8NHL6  (LIRB1_HUMAN) -  Leukocyte immunoglobulin-like receptor subfamily B member 1 from Homo sapiens

Seq: 650 a.a.

Struc: 192 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1016/S1074-7613(00)00071-6

Immunity 13:727-736 (2000)

PubMed id: 11114384

Crystal structure and ligand binding properties of the D1D2 region of the inhibitory receptor LIR-1 (ILT2).

T.L.Chapman, A.P.Heikema, A.P.West, P.J.Bjorkman.

ABSTRACT

LIR-1 is an inhibitory receptor that recognizes class I MHC molecules and the human cytomegalovirus class I homolog UL18. Here, we report the 2.1 A resolution crystal structure of the ligand binding portion of LIR-1 (domains 1 and 2 [D1D2]) and localize the binding region for UL18. LIR-1 D1D2 is composed of two immunoglobulin-like domains arranged at an acute angle to form a bent structure resembling the structures of natural killer inhibitory receptors (KIRs). The LIR-1 binding site comprises a portion of D1 distant from the interdomain hinge region that constitutes the KIR binding site, consistent with differences in LIR-1 and KIR recognition properties and functions.

Selected figure(s)

Figure 1.
Figure 1. LIR-1 D1D2 Crystal Structure(A) Ribbon diagram of the structure of LIR-1 D1D2. Disulfide bonds are shown in yellow, and dashed lines indicate disordered loops. Arrow indicates the location of the bond between residues 99 and 100, which can be proteolitically cleaved to generate stable fragments corresponding to D1 and D2 ([10]).(B) Topology diagram of LIR-1 D1D2. β strands are blue, 3[10] helices are green, and polyproline type II helices are red.(C) Stereoview of LIR-1 D1 (green) superimposed upon KIR2DL1 ([16]) (red). N and C termini of LIR-1 D1D2 are labeled. Cα atoms of the D1 domains of each structure were superimposed, illustrating the slight displacement of the D2 domains. Root mean square deviation (r.m.s.d) values for superpositions: 0.92 Å (71 Cα atoms) (LIR-1 D1 and KIR2DL1 D1), 1.25 Å (88 Cα atoms) (LIR-1 D2 and KIR2DL1 D2), 1.36 Å (67 Cα atoms) (LIR-1 D1 and LIR-1 D2).(D) LIR-1 D1D2 model in the region of the D1 3[10] helix superimposed on a 2.1 Å 2|F[obs]| − |F[calc]| annealed omit electron density map contoured at 1.0σ (map radius, 3.5 Å).

Figure 5.
Figure 5. Comparison of Ligand Binding Sites on LIR-1 D1D2 and KIR2DL1(A) Residues altered by site-directed mutagenesis are highlighted on a ribbon diagram of the LIR-1 D1D2 structure. Alteration of residues indicated in red resulted in changes in the affinity of LIR-1 D1D2 or LIR-2 D1D2 for UL18 (Table 2). Alteration of residues indicated in blue had no significant effect on the binding affinity.(B) Residues contributing to the KIR binding site for class I MHC molecules ([4, 42, 38, 43 and 6]) are highlighted on the structure of KIR2DL1 ( [16]).

The above figures are reprinted by permission from Cell Press: Immunity (2000, 13, 727-736) copyright 2000.

Figures were selected by an automated process.