3u3p: Difference between revisions
New page: '''Unreleased structure''' The entry 3u3p is ON HOLD 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. Descr... |
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The | ==The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)== | ||
<StructureSection load='3u3p' size='340' side='right'caption='[[3u3p]], [[Resolution|resolution]] 2.09Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3u3p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U3P FirstGlance]. <br> | |||
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3u3q|3u3q]], [[3u3s|3u3s]], [[3u3t|3u3t]], [[3u3v|3u3v]]</div></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TNFRSF21, DR6, UNQ437/PRO868 ([https://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=3u3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3p OCA], [https://pdbe.org/3u3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u3p RCSB], [https://www.ebi.ac.uk/pdbsum/3u3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3p ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[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;"> | |||
== 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<ref>PMID:22525750</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3u3p" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Tumor necrosis factor receptor 3D structures|Tumor necrosis factor receptor 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Human]] | |||
[[Category: Large Structures]] | |||
[[Category: Ding, W]] | |||
[[Category: Hung, L W]] | |||
[[Category: Jiao, L Y]] | |||
[[Category: Liu, Z J]] | |||
[[Category: Matsugaki, N]] | |||
[[Category: Ru, H]] | |||
[[Category: Shaw, N]] | |||
[[Category: Wakatsuki, S]] | |||
[[Category: Zhang, L G]] | |||
[[Category: Zhao, L X]] | |||
[[Category: Apoptosis]] | |||
[[Category: Trigger apoptosis]] | |||
Latest revision as of 08:56, 13 July 2022
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)
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 PubMedA 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 AlsoReferences
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