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.


2ims

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:19, 31 March 2021) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2ims.jpg|left|200px]]
 
-
{{Structure
+
==The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site==
-
|PDB= 2ims |SIZE=350|CAPTION= <scene name='initialview01'>2ims</scene>, resolution 1.48&Aring;
+
<StructureSection load='2ims' size='340' side='right'caption='[[2ims]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>
+
<table><tr><td colspan='2'>[[2ims]] 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=2IMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IMS FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
|GENE= BAK1, BAK, BCL2L7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
}}
+
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1maz|1maz]], [[1f16|1f16]], [[1lxl|1lxl]], [[1bxl|1bxl]], [[1mk3|1mk3]], [[1wsx|1wsx]], [[2imt|2imt]]</div></td></tr>
-
 
+
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BAK1, BAK, BCL2L7 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-
'''The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site'''
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ims FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ims OCA], [https://pdbe.org/2ims PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ims RCSB], [https://www.ebi.ac.uk/pdbsum/2ims PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ims ProSAT]</span></td></tr>
-
 
+
</table>
-
 
+
== Function ==
-
==Overview==
+
[[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>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/im/2ims_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ims ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
BAK/BAX-mediated mitochondrial outer-membrane permeabilization (MOMP) drives cell death during development and tissue homeostasis from zebrafish to humans. In most cancers, this pathway is inhibited by BCL-2 family antiapoptotic members, which bind and block the action of proapoptotic BCL proteins. We report the 1.5 A crystal structure of calpain-proteolysed BAK, cBAK, to reveal a zinc binding site that regulates its activity via homodimerization. cBAK contains an occluded BH3 peptide binding pocket that binds a BID BH3 peptide only weakly . Nonetheless, cBAK requires activation by truncated BID to induce cytochrome c release in mitochondria isolated from bak/bax double-knockout mouse embryonic fibroblasts. The BAK-mediated MOMP is inhibited by low micromolar zinc levels. This inhibition is alleviated by mutation of the zinc-coordination site in BAK. Our results link directly the antiapoptotic effects of zinc to BAK.
BAK/BAX-mediated mitochondrial outer-membrane permeabilization (MOMP) drives cell death during development and tissue homeostasis from zebrafish to humans. In most cancers, this pathway is inhibited by BCL-2 family antiapoptotic members, which bind and block the action of proapoptotic BCL proteins. We report the 1.5 A crystal structure of calpain-proteolysed BAK, cBAK, to reveal a zinc binding site that regulates its activity via homodimerization. cBAK contains an occluded BH3 peptide binding pocket that binds a BID BH3 peptide only weakly . Nonetheless, cBAK requires activation by truncated BID to induce cytochrome c release in mitochondria isolated from bak/bax double-knockout mouse embryonic fibroblasts. The BAK-mediated MOMP is inhibited by low micromolar zinc levels. This inhibition is alleviated by mutation of the zinc-coordination site in BAK. Our results link directly the antiapoptotic effects of zinc to BAK.
-
==About this Structure==
+
The X-ray structure of a BAK homodimer reveals an inhibitory zinc binding site.,Moldoveanu T, Liu Q, Tocilj A, Watson M, Shore G, Gehring K Mol Cell. 2006 Dec 8;24(5):677-88. PMID:17157251<ref>PMID:17157251</ref>
-
2IMS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMS OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
The X-ray structure of a BAK homodimer reveals an inhibitory zinc binding site., Moldoveanu T, Liu Q, Tocilj A, Watson M, Shore G, Gehring K, Mol Cell. 2006 Dec 8;24(5):677-88. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17157251 17157251]
+
</div>
-
[[Category: Homo sapiens]]
+
<div class="pdbe-citations 2ims" style="background-color:#fffaf0;"></div>
-
[[Category: Single protein]]
+
-
[[Category: Gehring, K B.]]
+
-
[[Category: Liu, Q.]]
+
-
[[Category: Moldoveanu, T.]]
+
-
[[Category: Shore, G C.]]
+
-
[[Category: Tocilj, A.]]
+
-
[[Category: Watson, M.]]
+
-
[[Category: ZN]]
+
-
[[Category: dimer]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:31:16 2008''
+
==See Also==
 +
*[[B-cell lymphoma proteins 3D structures|B-cell lymphoma proteins 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Human]]
 +
[[Category: Large Structures]]
 +
[[Category: Gehring, K B]]
 +
[[Category: Liu, Q]]
 +
[[Category: Moldoveanu, T]]
 +
[[Category: Shore, G C]]
 +
[[Category: Tocilj, A]]
 +
[[Category: Watson, M]]
 +
[[Category: Apoptosis]]
 +
[[Category: Dimer]]

Current revision

The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site

PDB ID 2ims

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ims"
Personal tools