PDBsum entry 2dli

Immune system

PDB id: 2dli

Contents

Protein chain

196 a.a. *

Waters ×10

* Residue conservation analysis

PDB id:

2dli

Name:

Immune system

Title:

Killer immunoglobulin receptor 2dl2,trigonal form

Structure:

Protein (mhc class i nk cell receptor precursor). Chain: a. Fragment: extracellular hla-cw3 recognition domain. Synonym: p58 natural killer cell receptor. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell: natural killer. Cellular_location: surface. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.90Å R-factor: 0.227 R-free: 0.331

Authors:

P.D.Sun,G.A.Snyder

Key ref:

G.A.Snyder et al. (1999). Crystal structure of the HLA-Cw3 allotype-specific killer cell inhibitory receptor KIR2DL2. Proc Natl Acad Sci U S A, 96, 3864-3869. PubMed id: 10097129 DOI: 10.1073/pnas.96.7.3864

Date:

08-Mar-99 Release date: 13-Jan-00

Protein chain

P43627  (KI2L2_HUMAN) -  Killer cell immunoglobulin-like receptor 2DL2 from Homo sapiens

Seq: 348 a.a.

Struc: 196 a.a.

DOI no: 10.1073/pnas.96.7.3864

Proc Natl Acad Sci U S A 96:3864-3869 (1999)

PubMed id: 10097129

Crystal structure of the HLA-Cw3 allotype-specific killer cell inhibitory receptor KIR2DL2.

G.A.Snyder, A.G.Brooks, P.D.Sun.

ABSTRACT

Killer cell inhibitory receptors (KIR) protect class I HLAs expressing target cells from natural killer (NK) cell-mediated lysis. To understand the molecular basis of this receptor-ligand recognition, we have crystallized the extracellular ligand-binding domains of KIR2DL2, a member of the Ig superfamily receptors that recognize HLA-Cw1, 3, 7, and 8 allotypes. The structure was determined in two different crystal forms, an orthorhombic P212121 and a trigonal P3221 space group, to resolutions of 3.0 and 2.9 A, respectively. The overall fold of this structure, like KIR2DL1, exhibits K-type Ig topology with cis-proline residues in both domains that define beta-strand switching, which sets KIR apart from the C2-type hematopoietic growth hormone receptor fold. The hinge angle of KIR2DL2 is approximately 80 degrees, 14 degrees larger than that observed in KIR2DL1 despite the existence of conserved hydrophobic residues near the hinge region. There is also a 5 degrees difference in the observed hinge angles in two crystal forms of 2DL2, suggesting that the interdomain hinge angle is not fixed. The putative ligand-binding site is formed by residues from several variable loops with charge distribution apparently complementary to that of HLA-C. The packing of the receptors in the orthorhombic crystal form offers an intriguing model for receptor aggregation on the cell surface.

Selected figure(s)

Figure 1.
Fig. 1. (A) Ribbon diagram of 2DL2 structure. The secondary structure assignment for the strands in D1 domain are A (8-12), A' (16-19), B (23-30), C (36-43), C' (46-52), D (53-56), E (60-67), F (75-82), and G (90-101). The strands for the D2 domain are: A (108-111), A' (116-119), B (123-130), C (135-142), C' (145-152), D (153-156), E (160-167), F (172-180), and G (188-198), respectively. This figure and other structural figures were prepared by using the program MOLSCRIPT 2.1 and RASTER3D (55, 56). The region around cis-Pro-14 (B) and cis-Pro-114 (C) shows the kink at the proline residue and the -hairpin.

Figure 2.
Fig. 2. (A) Stereo drawing showing the structure overlay between 2DL1 (in red) and 2DL2 (in green) with their D2 domains superimposed. The hinge angles, calculated with the program HINGE, are 66° and 80° for 2DL1 and 2DL2, respectively. Residues involved in the interdomain packing are shown. The coordinates are from the refined orthorhombic crystal form. (B) Overlay of refined 2DL2 structures from the orthorhombic (in green) and the trigonal (in blue) crystal forms.

Figures were selected by an automated process.