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3jbt

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Current revision (08:43, 7 February 2024) (edit) (undo)
 
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<SX load='3jbt' size='340' side='right' viewer='molstar' caption='[[3jbt]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
<SX load='3jbt' size='340' side='right' viewer='molstar' caption='[[3jbt]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3jbt]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus] and [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JBT FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3jbt]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JBT FirstGlance]. <br>
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</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APAF1, KIAA0413 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
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<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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=3jbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbt OCA], [https://pdbe.org/3jbt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jbt RCSB], [https://www.ebi.ac.uk/pdbsum/3jbt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbt ProSAT]</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=3jbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbt OCA], [https://pdbe.org/3jbt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jbt RCSB], [https://www.ebi.ac.uk/pdbsum/3jbt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbt ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://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> [[https://www.uniprot.org/uniprot/CYC_HORSE CYC_HORSE]] 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).
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[https://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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The apoptotic protease-activating factor 1 (Apaf-1) controls the onset of many known forms of intrinsic apoptosis in mammals. Apaf-1 exists in normal cells as an autoinhibited monomer. Upon binding to cytochrome c and dATP, Apaf-1 oligomerizes into a heptameric complex known as the apoptosome, which recruits and activates cell-killing caspases. Here we present an atomic structure of an intact mammalian apoptosome at 3.8 A resolution, determined by single-particle, cryo-electron microscopy (cryo-EM). Structural analysis, together with structure-guided biochemical characterization, uncovered how cytochrome c releases the autoinhibition of Apaf-1 through specific interactions with the WD40 repeats. Structural comparison with autoinhibited Apaf-1 revealed how dATP binding triggers a set of conformational changes that results in the formation of the apoptosome. Together, these results constitute the molecular mechanism of cytochrome c- and dATP-mediated activation of Apaf-1.
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Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1.,Zhou M, Li Y, Hu Q, Bai XC, Huang W, Yan C, Scheres SH, Shi Y Genes Dev. 2015 Nov 15;29(22):2349-61. doi: 10.1101/gad.272278.115. Epub 2015 Nov, 5. PMID:26543158<ref>PMID:26543158</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3jbt" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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</SX>
[[Category: Equus caballus]]
[[Category: Equus caballus]]
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[[Category: Human]]
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[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Bai, X]]
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[[Category: Bai X]]
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[[Category: Hu, Q]]
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[[Category: Hu Q]]
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[[Category: Huang, W]]
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[[Category: Huang W]]
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[[Category: Li, Y]]
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[[Category: Li Y]]
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[[Category: Scheres, S H.W]]
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[[Category: Scheres SHW]]
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[[Category: Shi, Y]]
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[[Category: Shi Y]]
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[[Category: Yan, C]]
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[[Category: Yan C]]
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[[Category: Zhou, M]]
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[[Category: Zhou M]]
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[[Category: Apaf-1]]
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[[Category: Apoptosis]]
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[[Category: Apoptosome]]
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[[Category: Cryo-em structure]]
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Current revision

Atomic structure of the Apaf-1 apoptosome

3jbt, resolution 3.80Å

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OCA

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