Figure 1.
Complex structure of engineered αL I domain and ICAM-1 D1.
(A&B) Schematic drawings of the integrin headpiece, denoting intra- and inter-domain rearrangements during the engagement of LFA-1 with ICAM-1. A structural transition from low (A) to high affinity conformation (B) involves downward displacement of the α7-helix, shape change in metal-ion coordination sites, and swing-out movement of the hybrid domain. SyMBS = synergistic metal binding site; MIDAS = metal-ion dependent adhesion site; ADMIDAS = adjacent to MIDAS. (C) Ribbon diagram of the engineered αL I domain (pale yellow), containing a substitution of F265S, in complex with the engineered domain 1 (D1) of ICAM-1 (light purple). The residues coordinating to the metal ion in the MIDAS, Ser-139, Ser-141, and Thr-206 in I domain and Glu-34 in ICAM-1 D1 are shown in stick models. The Mg2+ ion is shown as a pink sphere. (D) The electron density map, drawn together with cartoon or stick models, shows an open conformation of the β6-strand and the α7-helix. The three hydrophobic residues (Leu-289, Phe-292, and Leu-295; cyan) are shown in stick models. (E) In comparison to the previous open structures of the I domains of different α subunits, αM (1IDO; blue) [27] and α2 (1DZI; green) [28], the α7-helix in our structure (3TCX; magenta) shows a comparable extent of downward displacement, away from the closed structure seen in the wild-type αL I domain (3F74; yellow) [44]. (F) Ribbon diagrams of 14 complexes found in an asymmetric unit. I domains are drawn in grey, and 14 molecules of D1 are drawn in different colors for clarity. Dotted circles in cyan color indicate the interface between two C-terminal ends of D1. (G) Superimposed 14 complexes are shown as Ca-traces.
Figure 2.
Comparison with the previous complex structures of the αL I domain with ligands.
(A–C) Superimposed to the current αL I domain and ICAM-1 D1 structure (3TCX; magenta) are the previously solved complex structures of (A) high affinity (HA) αL I domain containingF265S/F292G with ICAM-5 D1D2 (3BN3; yellow) [26], (B) intermediate affinity (IA) αL I domain containing L161C/F299C with ICAM-1 D1D2 (1MQ8; blue) [17], and (C) high affinity (HA) αL I domain containing K287C/K294C with ICAM-3 D1 (1T0P; green) [20]. The acidic residue of the ICAMs (Glu-34 in ICAM-1 and Glu-37 in ICAM-3 and ICAM-5) docking into the I domains and the Mg2+ ions are shown as stick and spheres, respectively. The β5-α6 and β6-α7 loops are circled with dotted lines.
Table 1.
Data Collection and Refinement Statistics.
Figure 3.
Structural deviation in engineered ICAM-1 D1 and its implication in ICAM-1 interaction with LFA-1 and HRV.
(A) Cα-traces of engineered ICAM-1 D1 (magenta) and the wild-type D1 in D1D2 fragment (1IAM in yellow) are drawn with solvent-accessible surface plot (grey). (B) Hydrogen bond network formed by Thr-2, Thr-23, Ser-67, and Ser-74 at the N-terminal protein core is shown in grey dotted lines with distances in Å from the wild-type ICAM-1 structure (1IAM). Substitutions of T2V, S67A, and T23A in D1 are indicated. (C) A hydrogen bond between Pro-6 and Thr-78 is shown with a dotted line. Substitutions of P63V and T78A found in D1 are indicated. (D) D1 structures of the previous ICAM-1 D1D2 structures (1IAM in yellow [15], 1IC1 in blue [24], 1MQ8 in green [17]) were superimposed to engineered D1 (3TCX in magenta). The loops, B–C, D–E, and F–G, are circled with dotted lines. (E) The distances between the Cα atoms (dotted lines in magenta) of the triad Thr-2, Thr-23, and Ser-67, and the Cα distance between Pro-28 to Thr-23 in previous structures are compared with those in D1 mutant. (F) The superimposed ICAM-1 structures with the HRV were modeled based on the cryo-EM Cα coordinates of ICAM-1 D1D2 bound to HRV16 (1D3E [31] and 1AYM [45]). (G) The superimposed D1 structures are shown with the αL I domain shown as solvent-accessible surface.
Figure 4.
Differences in Cα positions for the superimposed structures of ICAM-1 D1.
Pair-wise Cα-Cα distances between wild-type ICAM-1 (1IAM, 1MQ8, and 1IC1) and engineered D1 (3TCX) are plotted. Also, Cα- Cα distances among the wild-type ICAM-1 structures are plotted (1IAM to 1MQ8, 1IC1 to 1IAM, and 1MQ8 to 1IC1). Putative interacting residues of ICAM-1 D1 with HRV16 capsid as well as the residues in close contact with the αL I domain are indicated with brackets and corresponding residue numbers. Arrow bars denote the residues that form the β-strands in ICAM-1 D1.