|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)== | | ==The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)== |
| - | <StructureSection load='3u3v' size='340' side='right' caption='[[3u3v]], [[Resolution|resolution]] 2.96Å' scene=''> | + | <StructureSection load='3u3v' size='340' side='right'caption='[[3u3v]], [[Resolution|resolution]] 2.96Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3u3v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U3V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3u3v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U3V FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3u3p|3u3p]], [[3u3q|3u3q]], [[3u3s|3u3s]], [[3u3t|3u3t]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.96Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TNFRSF21, DR6, UNQ437/PRO868 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3u3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3v OCA], [https://pdbe.org/3u3v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u3v RCSB], [https://www.ebi.ac.uk/pdbsum/3u3v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3v ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3u3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3v OCA], [http://pdbe.org/3u3v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3u3v RCSB], [http://www.ebi.ac.uk/pdbsum/3u3v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3v ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TNR21_HUMAN TNR21_HUMAN]] May activate NF-kappa-B and promote apoptosis. May activate JNK and be involved in T-cell differentiation. Required for both normal cell body death and axonal pruning. Trophic-factor deprivation triggers the cleavage of surface APP by beta-secretase to release sAPP-beta which is further cleaved to release an N-terminal fragment of APP (N-APP). N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6). | + | [https://www.uniprot.org/uniprot/TNR21_HUMAN TNR21_HUMAN] May activate NF-kappa-B and promote apoptosis. May activate JNK and be involved in T-cell differentiation. Required for both normal cell body death and axonal pruning. Trophic-factor deprivation triggers the cleavage of surface APP by beta-secretase to release sAPP-beta which is further cleaved to release an N-terminal fragment of APP (N-APP). N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 21: |
Line 20: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Tumor necrosis factor receptor|Tumor necrosis factor receptor]] | + | *[[Tumor necrosis factor receptor 3D structures|Tumor necrosis factor receptor 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Ding, W]] | + | [[Category: Large Structures]] |
| - | [[Category: Hung, L W]] | + | [[Category: Ding W]] |
| - | [[Category: Jiao, L Y]] | + | [[Category: Hung LW]] |
| - | [[Category: Liu, Z J]] | + | [[Category: Jiao LY]] |
| - | [[Category: Matsugaki, N]] | + | [[Category: Liu ZJ]] |
| - | [[Category: Ru, H]] | + | [[Category: Matsugaki N]] |
| - | [[Category: Shaw, N]] | + | [[Category: Ru H]] |
| - | [[Category: Wakatsuki, S]] | + | [[Category: Shaw N]] |
| - | [[Category: Zhang, L G]] | + | [[Category: Wakatsuki S]] |
| - | [[Category: Zhao, L X]] | + | [[Category: Zhang LG]] |
| - | [[Category: Apoptosis]]
| + | [[Category: Zhao LX]] |
| - | [[Category: Trigger apoptosis]]
| + | |
| Structural highlights
Function
TNR21_HUMAN May activate NF-kappa-B and promote apoptosis. May activate JNK and be involved in T-cell differentiation. Required for both normal cell body death and axonal pruning. Trophic-factor deprivation triggers the cleavage of surface APP by beta-secretase to release sAPP-beta which is further cleaved to release an N-terminal fragment of APP (N-APP). N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6).
Publication Abstract from PubMed
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.
S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS.,Ru H, Zhao L, Ding W, Jiao L, Shaw N, Liang W, Zhang L, Hung LW, Matsugaki N, Wakatsuki S, Liu ZJ Acta Crystallogr D Biol Crystallogr. 2012 May;68(Pt 5):521-30. Epub 2012 Apr 17. PMID:22525750[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ru H, Zhao L, Ding W, Jiao L, Shaw N, Liang W, Zhang L, Hung LW, Matsugaki N, Wakatsuki S, Liu ZJ. 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. Epub 2012 Apr 17. PMID:22525750 doi:10.1107/S0907444912004490
|
