3U3S: The S-sad Phased Crystal Structure Of The Ecto-domain Of Death Receptor 6 (dr6)

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), a comparative study was performed on data collected at wavelengths of 2.0 and 2.7 A. In spite of sub-optimal experimental conditions, the 2.7 A 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.
PDB ID: 3U3SDownload
MMDB ID: 99176
PDB Deposition Date: 2011/10/6
Updated in MMDB: 2013/07
Experimental Method:
x-ray diffraction
Resolution: 2.7  Å
Source Organism:
Similar Structures:
Biological Unit for 3U3S: dimeric; determined by author and by software (PISA)
Molecular Components in 3U3S
Label Count Molecule
Proteins (2 molecules)
Tumor Necrosis Factor Receptor Superfamily Member 21(Gene symbol: TNFRSF21)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB