5L81

Crystal structure of the PH domain of murine kindlin-3

5L81 の概要

• エントリーDOI: 10.2210/pdb5l81/pdb
• 分子名称: Fermitin family homolog 3, SODIUM ION (3 entities in total)
• 機能のキーワード: pleckstrin homology domain, membrane binding, integrin activation, signaling protein
• 由来する生物種: Mus musculus (Mouse)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 33811.45

構造登録者

Ni, T.,Harlos, K.,Gilbert, R.J.C. (登録日: 2016-06-06, 公開日: 2017-01-11, 最終更新日: 2024-01-10)

主引用文献

Ni, T.,Kalli, A.C.,Naughton, F.B.,Yates, L.A.,Naneh, O.,Kozorog, M.,Anderluh, G.,Sansom, M.S.,Gilbert, R.J.
Structure and lipid-binding properties of the kindlin-3 pleckstrin homology domain.
Biochem. J., 474:539-556, 2017

PubMed Abstract: Kindlins co-activate integrins alongside talin. They possess, like talin, a FERM domain (4.1-erythrin-radixin-moiesin domain) comprising F0-F3 subdomains, but with a pleckstrin homology (PH) domain inserted in the F2 subdomain that enables membrane association. We present the crystal structure of murine kindlin-3 PH domain determined at a resolution of 2.23 Å and characterise its lipid binding using biophysical and computational approaches. Molecular dynamics simulations suggest flexibility in the PH domain loops connecting β-strands forming the putative phosphatidylinositol phosphate (PtdInsP)-binding site. Simulations with PtdInsP-containing bilayers reveal that the PH domain associates with PtdInsP molecules mainly via the positively charged surface presented by the β1-β2 loop and that it binds with somewhat higher affinity to PtdIns(3,4,5)P compared with PtdIns(4,5)P Surface plasmon resonance (SPR) with lipid headgroups immobilised and the PH domain as an analyte indicate affinities of 300 µM for PtdIns(3,4,5)P and 1 mM for PtdIns(4,5)P In contrast, SPR studies with an immobilised PH domain and lipid nanodiscs as the analyte show affinities of 0.40 µM for PtdIns(3,4,5)P and no affinity for PtdIns(4,5)P when the inositol phosphate constitutes 5% of the total lipids (∼5 molecules per nanodisc). Reducing the PtdIns(3,4,5)P composition to 1% abolishes nanodisc binding to the PH domain, as does site-directed mutagenesis of two lysines within the β1-β2 loop. Binding of PtdIns(3,4,5)P by a canonical PH domain, Grp1, is not similarly influenced by SPR experimental design. These data suggest a role for PtdIns(3,4,5)P clustering in the binding of some PH domains and not others, highlighting the importance of lipid mobility and clustering for the biophysical assessment of protein-membrane interactions.

PubMed: 27974389
DOI: 10.1042/BCJ20160791

実験手法

X-RAY DIFFRACTION (2.23 Å)