Open AccessS‐SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS
Author(s) -
Ru Heng,
Zhao Lixia,
Ding Wei,
Jiao Lianying,
Shaw Neil,
Liang Wenguang,
Zhang Liguo,
Hung LiWei,
Matsugaki Naohiro,
Wakatsuki Soichi,
Liu ZhiJie
Publication year - 2012
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444912004490
Subject(s) - ectodomain , receptor , dimer , crystallography , phaser , chemistry , wavelength , biophysics , physics , biology , biochemistry , nuclear magnetic resonance , optics
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 Å), a comparative study was performed on data collected at wavelengths of 2.0 and 2.7 Å. In spite of sub‐optimal experimental conditions, the 2.7 Å 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.