PDBsum entry 4wk0

Cell adhesion/immune system

PDB id: 4wk0

Contents

Protein chains

449 a.a.

427 a.a.

Ligands

ARG-GLY-ASP

NAG-NAG-BMA-MAN-MAN-MAN

NAG-NAG ×4

NAG ×4

Metals

_CA ×6

_MG

Waters ×629

References listed in PDB file

Key reference

• Title: Metal ion and ligand binding of integrin α5β1.
• Authors: W.Xia, T.A.Springer.
• Ref.: Proc Natl Acad Sci U S A, 2014, 111, 17863-17868. [DOI no: 10.1073/pnas.1420645111]
• PubMed id: 25475857

Abstract

Integrin α5β1 binds to an Arg-Gly-Asp (RGD) motif in its ligand fibronectin. We report high-resolution crystal structures of a four-domain α5β1 headpiece fragment, alone or with RGD peptides soaked into crystals, and RGD peptide affinity measurements. The headpiece crystallizes in a closed conformation essentially identical to that seen previously for α5β1 complexed with a Fab that allosterically inhibits ligand binding by stabilizing the closed conformation. Soaking experiments show that binding of cyclic RGD peptide with 20-fold higher affinity than a linear RGD peptide induces conformational change in the β1-subunit βI domain to a state that is intermediate between closed (low affinity) and open (high affinity). In contrast, binding of a linear RGD peptide induces no shape shifting. However, linear peptide binding induces shape shifting when Ca(2+) is depleted during soaking. Ca(2+) bound to the adjacent to metal ion-dependent adhesion site (ADMIDAS), at the locus of shape shifting, moves and decreases in occupancy, correlating with an increase in affinity for RGD measured when Ca(2+) is depleted. The results directly demonstrate that Ca(2+) binding to the ADMIDAS stabilizes integrins in the low-affinity, closed conformation. Comparisons in affinity between four-domain and six-domain headpiece constructs suggest that flexible integrin leg domains contribute to conformational equilibria. High-resolution views of the hybrid domain interface with the plexin-semaphorin-integrin (PSI) domain in different orientations show a ball-and-socket joint with a hybrid domain Arg side chain that rocks in a PSI domain socket lined with carbonyl oxygens.