PDBsum entry 4wk2

Cell adhesion/immune system

PDB id: 4wk2

Contents

Protein chains

448 a.a.

427 a.a.

Ligands

GLY-ARG-GLY-ASP-SER-PRO

NAG-NAG-BMA-MAN-MAN-MAN-MAN

NAG-NAG ×4

NAG-NAG-BMA-MAN

NAG ×4

Metals

_CA ×6

_MG

Waters ×164

PDB id:

4wk2

Name:

Cell adhesion/immune system

Title:

Metal ion and ligand binding of integrin

Structure:

Integrin alpha-5. Chain: a. Fragment: unp residues 42-493. Synonym: cd49 antigen-like family member e,fibronectin receptor subunit alpha,integrin alpha-f,vla-5. Engineered: yes. Mutation: yes. Integrin beta-1. Chain: b.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: itga5, fnra. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek 293. Gene: itgb1, fnrb, mdf2, msk12. Synthetic: yes.

Resolution:

2.50Å R-factor: 0.212 R-free: 0.254

Authors:

W.Xia,T.A.Springer

Key ref:

W.Xia and T.A.Springer (2014). Metal ion and ligand binding of integrin α5β1. Proc Natl Acad Sci U S A, 111, 17863-17868. PubMed id: 25475857 DOI: 10.1073/pnas.1420645111

Date:

01-Oct-14 Release date: 03-Dec-14

Protein chain

P08648  (ITA5_HUMAN) -  Integrin alpha-5 from Homo sapiens

Seq: 1049 a.a.

Struc: 448 a.a.*

Protein chain

P05556  (ITB1_HUMAN) -  Integrin beta-1 from Homo sapiens

Seq: 798 a.a.

Struc: 427 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1073/pnas.1420645111

Proc Natl Acad Sci U S A 111:17863-17868 (2014)

PubMed id: 25475857

Metal ion and ligand binding of integrin α5β1.

W.Xia, T.A.Springer.

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.