PDBsum entry 3hi6

Cell adhesion/immune system

PDB id: 3hi6

Contents

Protein chains

180 a.a. *

213 a.a. *

210 a.a. *

Ligands

SO4 ×6

Metals

_MN ×2

Waters ×700

* Residue conservation analysis

PDB id:

3hi6

Name:

Cell adhesion/immune system

Title:

Crystal structure of intermediate affinity i domain of integrin lfa-1 with the fab fragment of its antibody al-57

Structure:

Integrin alpha-l. Chain: a, b. Fragment: unp residues 153-332. Synonym: leukocyte adhesion glycoprotein lfa-1 alpha chain, lfa-1a, leukocyte function-associated molecule 1 alpha chain, cd11 antigen- like family member a. Engineered: yes. Mutation: yes. Heavy chain of fab fragment of al-57 against alpha l i

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cd11a, itgal, lfa-1. Expressed in: escherichia coli. Expression_system_taxid: 562. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_taxid: 10029

Resolution:

2.30Å R-factor: 0.173 R-free: 0.226

Authors:

H.Zhang,J.Wang

Key ref:

H.Zhang et al. (2009). Structural basis of activation-dependent binding of ligand-mimetic antibody AL-57 to integrin LFA-1. Proc Natl Acad Sci U S A, 106, 18345-18350. PubMed id: 19805116 DOI: 10.1073/pnas.0909301106

Date:

19-May-09 Release date: 22-Sep-09

Protein chains

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

Seq: 1170 a.a.

Struc: 180 a.a.*

Protein chains

No UniProt id for this chain

Struc: 213 a.a.

Protein chains

No UniProt id for this chain

Struc: 210 a.a.

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

DOI no: 10.1073/pnas.0909301106

Proc Natl Acad Sci U S A 106:18345-18350 (2009)

PubMed id: 19805116

Structural basis of activation-dependent binding of ligand-mimetic antibody AL-57 to integrin LFA-1.

H.Zhang, J.H.Liu, W.Yang, T.Springer, M.Shimaoka, J.H.Wang.

ABSTRACT

The activity of integrin LFA-1 (alpha(L)beta(2)) to its ligand ICAM-1 is regulated through the conformational changes of its ligand-binding domain, the I domain of alpha(L) chain, from an inactive, low-affinity closed form (LA), to an intermediate-affinity form (IA), and then finally, to a high-affinity open form (HA). A ligand-mimetic human monoclonal antibody AL-57 (activated LFA-1 clone 57) was identified by phage display to specifically recognize the affinity-upregulated I domain. Here, we describe the crystal structures of the Fab fragment of AL-57 in complex with IA, as well as in its unligated form. We discuss the structural features conferring AL-57's strong selectivity for the high affinity, open conformation of the I domain. The AL-57-binding site overlaps the ICAM-1 binding site on the I domain. Furthermore, an antibody Asp mimics an ICAM Glu by forming a coordination to the metal-ion dependent adhesion site (MIDAS). The structure also reveals better shape complementarity and a more hydrophobic interacting interface in AL-57 binding than in ICAM-1 binding. The results explain AL-57's antagonistic mimicry of LFA-1's natural ligands, the ICAM molecules.

Selected figure(s)

Figure 2.
MIDAS of the I domain in different conformations. The MIDAS residues of the I domain are shown as stick models and colored with purple carbon atoms in IA in the AL-57/IA structure (A), green carbon atoms in HA in the ICAM-3/HA structure (B, PDB code 1T0P) and cyan carbon atoms in the unligated IA with closed conformation (C, PDB code 1MJN). Acidic residues from ligands D101 in AL-57 (A) and E37 in ICAM-3 (B), are also shown as stick models with yellow carbon atoms. All oxygen atoms are in red. Metal ions in the MIDAS are labeled and shown as spheres. Waters in MIDAS are shown as red spheres and labeled with a “w.” Coordination bonds are shown as dashed lines. Compared to the closed conformation in the unligated IA, in which D239 coordinated to the MIDAS metal ion directly (C), D239 in IA(A) or HA (B) coordinated to the metal ion via a water molecule and the metal ion shifted about 2.3Å and coordinated to T206 directly.

Figure 3.
(A) Interacting residues in the binding interface. Aromatic residues from AL-57, which contribute a significant level of hydrophobic interaction, are shown as stick models with yellow carbons. E241 from IA and R31(H) from AL-57, which form electrostatic interactions, are also shown as stick models with yellow carbons. The metal ion in MIDAS is shown as a purple sphere. D101(H) from AL-57 is shown as a stick model in yellow. (B) The movement of the C-terminal α7 helix in IA. The wild-type LA (PDB code 3F74), unligated IA (PDB code 1MJN), IA in the AL-57/IA complex, and HA in the ICAM-3/HA (PDB code 1T0P) complex, were superimposed and colored in gold, cyan, magenta, and green, respectively. For clarity, only the α1 helices, β6 strands, β6-α7 loops, and α7 helices are shown as Cα traces. The engineered disulfide bonds (Cys-161-Cys-299 in IA and Cys-287-Cys-294 in HA) are shown as stick models. Compared to unligated IA, the β6-α7 loop of IA in AL-57/IA complex moved downward like that observed in HA, indicating an open conformation.

Figures were selected by an automated process.