3U3T

The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)

Summary for 3U3T

• Entry DOI: 10.2210/pdb3u3t/pdb
• Related: 3U3P 3U3Q 3U3S 3U3V
• Descriptor: Tumor necrosis factor receptor superfamily member 21 (1 entity in total)
• Functional Keywords: trigger apoptosis, apoptosis
• Biological source: Homo sapiens (human)
• Cellular location: Membrane; Single-pass type I membrane protein (Probable): O75509
• Total number of polymer chains: 1
• Total formula weight: 34211.57

Authors

Ru, H.,Zhao, L.X.,Ding, W.,Jiao, L.Y.,Shaw, N.,Zhang, L.G.,Hung, L.W.,Matsugaki, N.,Wakatsuki, S.,Liu, Z.J. (deposition date: 2011-10-06, release date: 2012-05-02, Last modification date: 2012-07-11)

Primary citation

Ru, H.,Zhao, L.X.,Ding, W.,Jiao, L.Y.,Shaw, N.,Liang, W.,Zhang, L.G.,Hung, L.W.,Matsugaki, N.,Wakatsuki, S.,Liu, Z.J.
S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS
Acta Crystallogr.,Sect.D, 68:521-530, 2012

PubMed 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 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.

PubMed: 22525750
DOI: 10.1107/S0907444912004490

Experimental method

X-RAY DIFFRACTION (3.21 Å)