PDBsum entry 1xdd

Immune system

PDB id: 1xdd

Contents

Protein chains

182 a.a. *

Ligands

AAY ×2

Metals

_MG ×2

Waters ×277

* Residue conservation analysis

PDB id:

1xdd

Name:

Immune system

Title:

X-ray structure of lfa-1 i-domain in complex with lfa703 at 2.2a resolution

Structure:

Integrin alpha-l. Chain: a, b. Fragment: i-domain. Synonym: leukocyte adhesion glycoprotein lfa-1 alpha chain, lfa-1a, leukocyte function associated molecule 1, alpha chain, cd11a, alphalbeta2, cd11a/cd18. Engineered: yes

Source:

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

Resolution:

2.20Å R-factor: 0.164 R-free: 0.206

Authors:

G.Weitz-Schmidt,K.Welzenbach,J.Dawson,J.Kallen

Key ref:

G.Weitz-Schmidt et al. (2004). Improved lymphocyte function-associated antigen-1 (LFA-1) inhibition by statin derivatives: molecular basis determined by x-ray analysis and monitoring of LFA-1 conformational changes in vitro and ex vivo. J Biol Chem, 279, 46764-46771. PubMed id: 15304496 DOI: 10.1074/jbc.M407951200

Date:

06-Sep-04 Release date: 21-Sep-04

Protein chains

P20701  (ITAL_HUMAN) -  Integrin alpha-L from Homo sapiens

Seq: 1170 a.a.

Struc: 182 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.M407951200

J Biol Chem 279:46764-46771 (2004)

PubMed id: 15304496

Improved lymphocyte function-associated antigen-1 (LFA-1) inhibition by statin derivatives: molecular basis determined by x-ray analysis and monitoring of LFA-1 conformational changes in vitro and ex vivo.

G.Weitz-Schmidt, K.Welzenbach, J.Dawson, J.Kallen.

ABSTRACT

The integrin lymphocyte function-associated antigen-1 (LFA-1) (alphaLbeta2; CD11a/CD18) plays an important role in leukocyte migration and T cell activation. LFA-1 is inhibited by the cholesterol-lowering drug lovastatin, which binds to an allosteric site of the alphaL I domain termed the lovastatin site (L-site). Here we report for the first time the x-ray structures of the LFA-1 I domain complexed with derivatives of lovastatin optimized for LFA-1 inhibition. This analysis identified two new subpockets within the L-site occupied by chemical groups of the statin derivatives but not by lovastatin itself. Occupancy of these L-site subpockets led to distinct conformational changes in LFA-1, which were detectable by an epitope-monitoring assay. We utilized this assay to demonstrate improved LFA-1 inhibition in human blood in vitro and in blood samples from treated animals ex vivo. Moreover, we demonstrate that the novel lovastatin-derived LFA-1 inhibitor LFA878 exhibits potent anti-inflammatory effects in carrageenan-induced rat paw edema. In summary, the findings reported here extend the understanding of LFA-1 inhibition at the molecular level, allow for the identification and design of LFA-1 inhibitors of further enhanced potency, and support the expectation that LFA-1 inhibitors binding to the L-site will be of therapeutic value in treating inflammatory diseases.

Selected figure(s)

Figure 2.
FIG. 2. X-ray structures of the complexes [L] I domain/LFA703 and [L] I domain/LFA878. A, stereo image of the L-site for [L] I domain/LFA703. I domain residues and ribbon representation are in white, LFA703 in cyan (oxygens are red, and nitrogens are blue). The substituted naphthyl group of LFA703 occupies a region (the naphthyl subpocket, colored magenta) formed mainly by Val130, Thr231, Val233, and Ile^255. B, stereo image of the L-site for [L] I domain/LFA878 (coloring as for LFA703). The veratryl group of LFA878 occupies a region (the veratrylsubpocket, colored magenta) formed mainly by Tyr257, Glu284, and Phe^285. A comparison with the I domain/LFA703 complex shows that Glu284 has dramatically changed its side-chain conformation. C, F[o] - F[c] electron density (contour level 3 , 8-2.2 Å) before LFA703 was inserted into the model. Superposed is the final model of LFA703 (carbons are cyan/yellow, oxygens are red, and nitrogens are blue). The naphthyl group adopts two alternate conformations. D, F[o] (contour - F[c] density level 3 electron , 8-2.1 Å) before LFA878 was inserted into the model. Superposed is the final model of LFA878 (coloring as for LFA703). E, superposition of LFA703 (carbons are yellow), LFA878 (carbons are cyan), and lovastatin (carbons are white) using C atoms of the respective [L] I domains. The decalin moieties occupy practically identical positions. F, MIDAS site for [L] I domain/LFA703. Final 2F[o] - F[c] electron density (contour level 3 , 8-2.2 Å) is shown in blue; carbons are yellow, oxygens are red, nitrogens are blue, water molecules are white, and the Mg2+ ion is cyan. Selected hydrogen bonds are shown as black lines (dashed lines for the interaction with neighboring molecule). Because of the direct coordination by Asp239, the electrophilicity of Mg2+ is reduced so that a glutamate (Glu218, colored magenta) from a neighboring molecule is only interacting indirectly (via a water molecule) with the Mg2+ in the MIDAS site. Single letter amino acid abbreviations are used with position numbers throughout the figure.

Figure 3.
FIG. 3. Lovastatin and LFA878 inhibit the binding of mAb R7.1 to LFA-1 in human blood in vitro. The binding of fluorescein isothiocyanate-labeled mAb R7.1 to leukocytes in human whole blood was quantified in the presence of lovastatin (Lov.) (100 µM) (A) or LFA878 (30 µM) (B) by flow cytometry as described under "Experimental Procedures." Red profiles indicate the binding of mAb R7.1 to lymphocytes, granulocytes, or monocytes in the presence of compound; black profiles such binding in the presence of the solvent control. A representative experiment is shown.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 46764-46771) copyright 2004.

Figures were selected by an automated process.