3u3p

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

3u3p is a 1 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	3u3q, 3u3s, 3u3t, 3u3v
Gene:	TNFRSF21, DR6, UNQ437/PRO868 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3u3p"

@@ Line 1: / Line 1: @@
 ==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]] 2.09&Aring;' scene=''>
+<StructureSection load='3u3p' size='340' side='right'caption='[[3u3p]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3u3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U3P FirstGlance]. <br>
+<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">[[3u3q|3u3q]], [[3u3s|3u3s]], [[3u3t|3u3t]], [[3u3v|3u3v]]</td></tr>
+</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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3u3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u3p RCSB], [http://www.ebi.ac.uk/pdbsum/3u3p PDBsum]</span></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 ==
-[[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;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, 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|Tumor necrosis factor receptor]]
+*[[Tumor necrosis factor receptor 3D structures|Tumor necrosis factor receptor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Homo sapiens]]
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Ding, W]]
 [[Category: Hung, L W]]

3u3p

From Proteopedia

Current revision

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

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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