7ofo: Difference between revisions

Revision as of 11:18, 14 June 2023

NMR structure of the Bak transmembrane helix in lipid nanodiscs

Structural highlights

7ofo is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BAK_HUMAN In the presence of an appropriate stimulus, accelerates programmed cell death by binding to, and antagonizing the anti-apoptotic action of BCL2 or its adenovirus homolog E1B 19k protein. Low micromolar levels of zinc ions inhibit the promotion of apoptosis.^[1] ^[2]

Publication Abstract from PubMed

Permeabilization of the outer mitochondrial membrane by pore-forming Bcl2 proteins is a crucial step for the induction of apoptosis. Despite a large set of data suggesting global conformational changes within pro-apoptotic Bak during pore formation, high-resolution structural details in a membrane environment remain sparse. Here, we used NMR and HDX-MS (Hydrogen deuterium exchange mass spectrometry) in lipid nanodiscs to gain important high-resolution structural insights into the conformational changes of Bak at the membrane that are dependent on a direct activation by BH3-only proteins. Furthermore, we determined the first high-resolution structure of the Bak transmembrane helix. Upon activation, alpha-helix 1 in the soluble domain of Bak dissociates from the protein and adopts an unfolded and dynamic potentially membrane-bound state. In line with this finding, comparative protein folding experiments with Bak and anti-apoptotic BclxL suggest that alpha-helix 1 in Bak is a metastable structural element contributing to its pro-apoptotic features. Consequently, mutagenesis experiments aimed at stabilizing alpha-helix 1 yielded Bak variants with delayed pore-forming activity. These insights will contribute to a better mechanistic understanding of Bak-mediated membrane permeabilization.

High-resolution analysis of the conformational transition of pro-apoptotic Bak at the lipid membrane.,Sperl LE, Ruhrnossl F, Schiller A, Haslbeck M, Hagn F EMBO J. 2021 Oct 18;40(20):e107159. doi: 10.15252/embj.2020107159. Epub 2021 Sep , 15. PMID:34523144^[3]

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

References

↑ Chittenden T, Flemington C, Houghton AB, Ebb RG, Gallo GJ, Elangovan B, Chinnadurai G, Lutz RJ. A conserved domain in Bak, distinct from BH1 and BH2, mediates cell death and protein binding functions. EMBO J. 1995 Nov 15;14(22):5589-96. PMID:8521816
↑ Moldoveanu T, Liu Q, Tocilj A, Watson M, Shore G, Gehring K. The X-ray structure of a BAK homodimer reveals an inhibitory zinc binding site. Mol Cell. 2006 Dec 8;24(5):677-88. PMID:17157251 doi:10.1016/j.molcel.2006.10.014
↑ Sperl LE, Ruhrnossl F, Schiller A, Haslbeck M, Hagn F. High-resolution analysis of the conformational transition of pro-apoptotic Bak at the lipid membrane. EMBO J. 2021 Oct 18;40(20):e107159. doi: 10.15252/embj.2020107159. Epub 2021 Sep , 15. PMID:34523144 doi:https://dx.doi.org/10.15252/embj.2020107159

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Chittenden T, Flemington C, Houghton AB, Ebb RG, Gallo GJ, Elangovan B, Chinnadurai G, Lutz RJ. A conserved domain in Bak, distinct from BH1 and BH2, mediates cell death and protein binding functions. EMBO J. 1995 Nov 15;14(22):5589-96. PMID:8521816

[2] Moldoveanu T, Liu Q, Tocilj A, Watson M, Shore G, Gehring K. The X-ray structure of a BAK homodimer reveals an inhibitory zinc binding site. Mol Cell. 2006 Dec 8;24(5):677-88. PMID:17157251 doi:10.1016/j.molcel.2006.10.014

[3] Sperl LE, Ruhrnossl F, Schiller A, Haslbeck M, Hagn F. High-resolution analysis of the conformational transition of pro-apoptotic Bak at the lipid membrane. EMBO J. 2021 Oct 18;40(20):e107159. doi: 10.15252/embj.2020107159. Epub 2021 Sep , 15. PMID:34523144 doi:https://dx.doi.org/10.15252/embj.2020107159

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==NMR structure of the Bak transmembrane helix in lipid nanodiscs==
-<StructureSection load='7ofo' size='340' side='right'caption='[[7ofo]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='7ofo' size='340' side='right'caption='[[7ofo]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7ofo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OFO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7ofo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OFO 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;'>[[7ofm|7ofm]]</div></td></tr>
+</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=7ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ofo OCA], [https://pdbe.org/7ofo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ofo RCSB], [https://www.ebi.ac.uk/pdbsum/7ofo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ofo ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BAK1, BAK, BCL2L7, CDN1 ([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=7ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ofo OCA], [https://pdbe.org/7ofo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ofo RCSB], [https://www.ebi.ac.uk/pdbsum/7ofo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ofo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/BAK_HUMAN BAK_HUMAN]] In the presence of an appropriate stimulus, accelerates programmed cell death by binding to, and antagonizing the anti-apoptotic action of BCL2 or its adenovirus homolog E1B 19k protein. Low micromolar levels of zinc ions inhibit the promotion of apoptosis.<ref>PMID:8521816</ref> <ref>PMID:17157251</ref>
+[https://www.uniprot.org/uniprot/BAK_HUMAN BAK_HUMAN] In the presence of an appropriate stimulus, accelerates programmed cell death by binding to, and antagonizing the anti-apoptotic action of BCL2 or its adenovirus homolog E1B 19k protein. Low micromolar levels of zinc ions inhibit the promotion of apoptosis.<ref>PMID:8521816</ref> <ref>PMID:17157251</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 17: @@
 </div>
 <div class="pdbe-citations 7ofo" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[B-cell lymphoma proteins 3D structures|B-cell lymphoma proteins 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Hagn, F]]
+[[Category: Hagn F]]
-[[Category: Sperl, L E]]
+[[Category: Sperl LE]]
-[[Category: Apoptosis]]
-[[Category: Bcl2 protein]]
-[[Category: Mitochondria]]
-[[Category: Pore formation]]

7ofo: Difference between revisions

Revision as of 11:18, 14 June 2023

NMR structure of the Bak transmembrane helix in lipid nanodiscs

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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