This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4v4l

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 19:20, 10 April 2020

Structure of the Drosophila apoptosome

4v4l, resolution 6.90Å

Structural highlights

4v4l is a 16 chain structure with sequence from Drome. This structure supersedes the now removed PDB entries 1vt4 and 3iz8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	Ark, CG6829, dapaf-1L, Dmel_CG6829, Hac1 (DROME)
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

The Drosophila Apaf-1 related killer forms an apoptosome in the intrinsic cell death pathway. In this study we show that Dark forms a single ring when initiator procaspases are bound. This Dark-Dronc complex cleaves DrICE efficiently; hence, a single ring represents the Drosophila apoptosome. We then determined the 3D structure of a double ring at approximately 6.9 A resolution and created a model of the apoptosome. Subunit interactions in the Dark complex are similar to those in Apaf-1 and CED-4 apoptosomes, but there are significant differences. In particular, Dark has "lost" a loop in the nucleotide-binding pocket, which opens a path for possible dATP exchange in the apoptosome. In addition, caspase recruitment domains (CARDs) form a crown on the central hub of the Dark apoptosome. This CARD geometry suggests that conformational changes will be required to form active Dark-Dronc complexes. When taken together, these data provide insights into apoptosome structure, function, and evolution.

Structure of the Drosophila apoptosome at 6.9 a resolution.,Yuan S, Yu X, Topf M, Dorstyn L, Kumar S, Ludtke SJ, Akey CW Structure. 2011 Jan 12;19(1):128-40. PMID:21220123^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yuan S, Yu X, Topf M, Dorstyn L, Kumar S, Ludtke SJ, Akey CW. Structure of the Drosophila apoptosome at 6.9 a resolution. Structure. 2011 Jan 12;19(1):128-40. PMID:21220123 doi:10.1016/j.str.2010.10.009

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4v4l"

@@ Line 3: / Line 3: @@
 <SX load='4v4l' size='340' side='right' viewer='molstar' caption='[[4v4l]], [[Resolution|resolution]] 6.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4v4l]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vt4 1vt4] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3iz8 3iz8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V4L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V4L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4v4l]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vt4 1vt4] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3iz8 3iz8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V4L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4V4L FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ark, CG6829, dapaf-1L, Dmel_CG6829, Hac1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=4v4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v4l OCA], [http://pdbe.org/4v4l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v4l RCSB], [http://www.ebi.ac.uk/pdbsum/4v4l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v4l ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4v4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v4l OCA], [http://pdbe.org/4v4l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v4l RCSB], [http://www.ebi.ac.uk/pdbsum/4v4l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v4l ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">

4v4l

From Proteopedia

Revision as of 19:20, 10 April 2020

Structure of the Drosophila apoptosome

Structural highlights

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox