3u3v

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

3u3v is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.96Å
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/3u3v"

@@ Line 3: / Line 3: @@
 <StructureSection load='3u3v' size='340' side='right'caption='[[3u3v]], [[Resolution|resolution]] 2.96&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3u3v]] 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=3U3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/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"><div style='overflow: auto; max-height: 3em;'>[[3u3p|3u3p]], [[3u3q|3u3q]], [[3u3s|3u3s]], [[3u3t|3u3t]]</div></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]] 2.96&#8491;</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=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>
 </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).
+[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 26: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Ding, W]]
+[[Category: Ding W]]
-[[Category: Hung, L W]]
+[[Category: Hung LW]]
-[[Category: Jiao, L Y]]
+[[Category: Jiao LY]]
-[[Category: Liu, Z J]]
+[[Category: Liu ZJ]]
-[[Category: Matsugaki, N]]
+[[Category: Matsugaki N]]
-[[Category: Ru, H]]
+[[Category: Ru H]]
-[[Category: Shaw, N]]
+[[Category: Shaw N]]
-[[Category: Wakatsuki, S]]
+[[Category: Wakatsuki S]]
-[[Category: Zhang, L G]]
+[[Category: Zhang LG]]
-[[Category: Zhao, L X]]
+[[Category: Zhao LX]]
-[[Category: Apoptosis]]
-[[Category: Trigger apoptosis]]

3u3v

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

Personal tools

Navigation

Search

Toolbox