PDBsum entry 1n3y

Cell adhesion

PDB id: 1n3y

Contents

Protein chain

189 a.a. *

Waters ×291

* Residue conservation analysis

PDB id:

1n3y

Name:

Cell adhesion

Title:

Crystal structure of the alpha-x beta2 integrin i domain

Structure:

Integrin alpha-x. Chain: a. Fragment: i domain. Synonym: leukocyte adhesion glycoprotein p150,95 alpha chain. Leukocyte adhesion receptor p150,95. Cd11c. Leu m5. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: itgax or cd11c. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.65Å R-factor: 0.209 R-free: 0.225

Authors:

T.Vorup-Jensen,C.Ostermeier,M.Shimaoka,U.Hommel,T.A.Springer

Key ref:

T.Vorup-Jensen et al. (2003). Structure and allosteric regulation of the alpha X beta 2 integrin I domain. Proc Natl Acad Sci U S A, 100, 1873-1878. PubMed id: 12554829 DOI: 10.1073/pnas.0237387100

Date:

30-Oct-02 Release date: 18-Feb-03

Protein chain

P20702  (ITAX_HUMAN) -  Integrin alpha-X from Homo sapiens

Seq: 1163 a.a.

Struc: 189 a.a.

DOI no: 10.1073/pnas.0237387100

Proc Natl Acad Sci U S A 100:1873-1878 (2003)

PubMed id: 12554829

Structure and allosteric regulation of the alpha X beta 2 integrin I domain.

T.Vorup-Jensen, C.Ostermeier, M.Shimaoka, U.Hommel, T.A.Springer.

ABSTRACT

The integrin alpha X beta 2 (CD11c/CD18, p150,95) binds ligands through the I domain of the alpha X subunit. Ligands include the complement factor fragment iC3b, a key component in the innate immune defense, which, together with the expression of alpha X beta 2 on dendritic cells and on other leukocytes, suggests a role in the immune response. We now report the structure of the alpha X I domain resolved at 1.65 A by x-ray crystallography. To analyze structural requirements for ligand binding we made a mutation in the alpha X I domain C-terminal helix, which increased the affinity for iC3b approximately 200-fold to 2.4 microM compared with the wild-type domain affinity of approximately 400 microM. Gel permeation chromatography supported a conformational change between the wild-type and mutated domains. Conservation of allosteric regulation in the alpha X I domain points to the functional importance of this phenomenon.

Selected figure(s)

Figure 1.
Fig. 1. The X I domain structure and comparison to the M I domain. (A-D) Comparison of X (cyan) and the M (magenta) I domains. The MIDAS metal ion present only in M is shown as a magenta sphere, and the water molecule oxygen present only in the X MIDAS is shown as a cyan sphere. (A) Backbones of X and M. (B) MIDAS region of the X and M I domains. Residue numbers refer to the X sequence. (C) Residues in proximity of the X and M MIDAS, which form part of a putative ligand-binding interface and differ in structure or polarity between the two I domains ( X and M residues are labeled in roman and italics, respectively). (D) Detail of the region forming the hydrophobic socket for Ile-314 ( X) or Ile-316 ( M). Residue numbers refer to the X sequence, and Leu-164 of M is labeled in italics. All figures were made with RIBBONS software (41). (E and F) Electrostatic surfaces of the M and X I domains. The molecular surfaces of the domains were constructed with GRASP (42). The electrostatic potentials were calculated with the Delphi algorithm (43) and mapped onto the molecular surfaces on a scale from 10 kT/e^ (red) to +10 kT/e^ (blue). A Mg2+ ion was placed at the X I domain MIDAS to make the electrostatic surfaces comparable. Positions of the metal ions in the X and M I domains are indicated with arrows.

Figure 2.
Fig. 2. Comparisons among closed I domain structures of the C-terminal -strand and -helix and overall secondary structure. (A) The C-terminal 6-strand and 7-helix. Superposition is based on the entire domain. The backbone segments shown are X, residues 288-317; M, residues 290-318 of 1JLM (15); 2, residues 306-334 of 1AOX (14); and L, residues 280-308 of 1LFA (16). The side chains of Ile-332 in 2, Ile-316 in M, Ile-314 in X, and Ile-306 in L are shown. (B) Structure-based sequence alignment of the X, M, L, and 2 I domains. The same closed structures as above were superimposed. [402]alpha -Helices are shown in gold and [403]beta -strands are shown in cyan. Secondary structure assignment was by the DSSP algorithm (44) from the structural coordinates.

Figures were selected by an automated process.