3cm6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:58, 1 November 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3cm6.png|left|200px]]
 
-
<!--
+
==Crystal structure of cell-death related nuclease 4 (CRN-4) bound with Er==
-
The line below this paragraph, containing "STRUCTURE_3cm6", creates the "Structure Box" on the page.
+
<StructureSection load='3cm6' size='340' side='right'caption='[[3cm6]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3cm6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CM6 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ER3:ERBIUM+(III)+ION'>ER3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
{{STRUCTURE_3cm6| PDB=3cm6 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cm6 OCA], [https://pdbe.org/3cm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cm6 RCSB], [https://www.ebi.ac.uk/pdbsum/3cm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cm6 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/CRN4_CAEEL CRN4_CAEEL] Involved in the degradation of chromosomal DNA. Contributes to cell killing.
 +
== 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/cm/3cm6_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=3cm6 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Cell death related nuclease 4 (CRN-4) is one of the apoptotic nucleases involved in DNA degradation in Caenorhabditis elegans. To understand how CRN-4 is involved in apoptotic DNA fragmentation, we analyzed CRN-4's biochemical properties, in vivo cell functions, and the crystal structures of CRN-4 in apo-form, Mn(2+)-bound active form, and Er(3+)-bound inactive form. CRN-4 is a dimeric nuclease with the optimal enzyme activity in cleaving double-stranded DNA in apoptotic salt conditions. Both mutational studies and the structures of the Mn(2+)-bound CRN-4 revealed the geometry of the functional nuclease active site in the N-terminal DEDDh domain. The C-terminal domain, termed the Zn-domain, contains basic surface residues ideal for nucleic acid recognition and is involved in DNA binding, as confirmed by deletion assays. Cell death analysis in C. elegans further demonstrated that both the nuclease active site and the Zn-domain are required for crn-4's function in apoptosis. Combining all of the data, we suggest a structural model where chromosomal DNA is bound at the Zn-domain and cleaved at the DEDDh nuclease domain in CRN-4 when the cell is undergoing apoptosis.
-
===Crystal structure of cell-death related nuclease 4 (CRN-4) bound with Er===
+
Crystal Structure of CRN-4: Implications for Domain Function in Apoptotic DNA Degradation.,Hsiao YY, Nakagawa A, Shi Z, Mitani S, Xue D, Yuan HS Mol Cell Biol. 2009 Jan;29(2):448-57. Epub 2008 Nov 3. PMID:18981218<ref>PMID:18981218</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_18981218}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3cm6" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 18981218 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18981218}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
3CM6 is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CM6 OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:18981218</ref><references group="xtra"/>
+
[[Category: Caenorhabditis elegans]]
[[Category: Caenorhabditis elegans]]
-
[[Category: Hsiao, Y Y.]]
+
[[Category: Large Structures]]
-
[[Category: Yuan, H S.]]
+
[[Category: Hsiao Y-Y]]
-
[[Category: 3'-5' exonuclease]]
+
[[Category: Yuan HS]]
-
[[Category: Apoptosis]]
+
-
[[Category: Apoptotic nuclease]]
+
-
[[Category: Dedd family]]
+
-
[[Category: Hydrolase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:59:51 2010''
+

Current revision

Crystal structure of cell-death related nuclease 4 (CRN-4) bound with Er

PDB ID 3cm6

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/3cm6"
Personal tools