S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS.Acta Crystallogr D Biol Crystallogr.2012 May;68(Pt 5):521-30

Acta Crystallogr D Biol Crystallogr, 2012 May;68(Pt 5):521-30. Epub 2012 Apr 17. doi:10.1107/S0907444912004490

S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS.

Heng Ru,a,b+ Lixia Zhao,a++ Wei Ding,a+++ Lianying Jiao,a Neil Shaw,a,c Wenguang Liang,a Liguo Zhang,a Li-Wei Hung,d Naohiro Matsugaki,e Soichi Wakatsukie and Zhi-Jie Liua,c*

Abstract

A subset of tumour necrosis factor receptor (TNFR) superfamily members contain death domains in their cytoplasmic tails. Death receptor 6 (DR6) is one such member and can trigger apoptosis upon the binding of a ligand by its cysteine-rich domains (CRDs). The crystal structure of the ectodomain (amino acids 1-348) of human death receptor 6 (DR6) encompassing the CRD region was phased using the anomalous signal from S atoms. In order to explore the feasibility of S-SAD phasing at longer wavelengths (beyond 2.5 ?), a comparative study was performed on data collected at wavelengths of 2.0 and 2.7 ?. In spite of sub-optimal experimental conditions, the 2.7 ? wavelength used for data collection showed potential for S-SAD phasing. The results showed that the R(ano)/R(p.i.m.) ratio is a good indicator for monitoring the anomalous data quality when the anomalous signal is relatively strong, while d''/sig(d'') calculated by SHELXC is a more sensitive and stable indicator applicable for grading a wider range of anomalous data qualities. The use of the `parameter-space screening method' for S-SAD phasing resulted in solutions for data sets that failed during manual attempts. SAXS measurements on the ectodomain suggested that a dimer defines the minimal physical unit of an unliganded DR6 molecule in solution.

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