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{{STRUCTURE_3j2t| PDB=3j2t  | SCENE= }}
==An improved model of the human apoptosome==
===An improved model of the human apoptosome===
<StructureSection load='3j2t' size='340' side='right' caption='[[3j2t]], [[Resolution|resolution]] 9.50&Aring;' scene=''>
{{ABSTRACT_PUBMED_23521171}}
== Structural highlights ==
<table><tr><td colspan='2'>[[3j2t]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3iyt 3iyt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J2T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J2T FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Apaf-1, APAF1, KIAA0413 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3j2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j2t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j2t RCSB], [http://www.ebi.ac.uk/pdbsum/3j2t PDBsum]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Apoptosome assembly is highly regulated in the intrinsic cell death pathway. To better understand this step, we created an improved model of the human apoptosome using a crystal structure of full length Apaf-1 and a single particle, electron density map at approximately 9.5 A resolution. The apoptosome model includes N-terminal domains of Apaf-1, cognate beta-propellers, and cytochrome c. A direct comparison of Apaf-1 in the apoptosome and as a monomer reveals conformational changes that occur during the first two steps of assembly. This includes an induced-fit mechanism for cytochrome c binding to regulatory beta-propellers, which is dependent on shape and charge complementarity, and a large rotation of the nucleotide binding module during nucleotide exchange. These linked conformational changes create an extended Apaf-1 monomer and drive apoptosome assembly. Moreover, the N-terminal CARD in the inactive Apaf-1 monomer is not shielded from other proteins by beta-propellers. Hence, the Apaf-1 CARD may be free to interact with a procaspase-9 CARD either before or during apoptosome assembly. Irrespective of the timing, the end product of assembly is a holo-apoptosome with an acentric CARD-CARD disk and tethered pc-9 catalytic domains. Subsequent activation of pc-9 leads to a proteolytic cascade and cell death.


==Function==
Changes in apaf-1 conformation that drive apoptosome assembly.,Yuan S, Topf M, Reubold TF, Eschenburg S, Akey CW Biochemistry. 2013 Apr 2;52(13):2319-27. doi: 10.1021/bi301721g. Epub 2013 Mar, 22. PMID:23521171<ref>PMID:23521171</ref>
[[http://www.uniprot.org/uniprot/APAF_HUMAN APAF_HUMAN]] Oligomeric Apaf-1 mediates the cytochrome c-dependent autocatalytic activation of pro-caspase-9 (Apaf-3), leading to the activation of caspase-3 and apoptosis. This activation requires ATP. Isoform 6 is less effective in inducing apoptosis.<ref>PMID:10393175</ref> <ref>PMID:12804598</ref> [[http://www.uniprot.org/uniprot/CYC_BOVIN CYC_BOVIN]] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.  Plays a role in apoptosis. Suppression of the anti-apoptotic members or activation of the pro-apoptotic members of the Bcl-2 family leads to altered mitochondrial membrane permeability resulting in release of cytochrome c into the cytosol. Binding of cytochrome c to Apaf-1 triggers the activation of caspase-9, which then accelerates apoptosis by activating other caspases (By similarity).


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[3j2t]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entries  and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3iyt 3iyt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J2T OCA].
</div>


==Reference==
==See Also==
<ref group="xtra">PMID:020462491</ref><references group="xtra"/><references/>
*[[Cytochrome c|Cytochrome c]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Akey, C W.]]
[[Category: Akey, C W]]
[[Category: Topf, M.]]
[[Category: Topf, M]]
[[Category: Yuan, S.]]
[[Category: Yuan, S]]
[[Category: Apaf-1]]
[[Category: Apaf-1]]
[[Category: Apoptosis]]
[[Category: Apoptosis]]
[[Category: Apoptosis protease activating factor-1]]
[[Category: Apoptosis protease activating factor-1]]
[[Category: Cytochrome c]]
[[Category: Cytochrome c]]
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