3mud: Difference between revisions

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-{{Seed}}
-[[Image:3mud.jpg|left|200px]]
-<!--
+==Structure of the Tropomyosin Overlap Complex from Chicken Smooth Muscle==
-The line below this paragraph, containing "STRUCTURE_3mud", creates the "Structure Box" on the page.
+<StructureSection load='3mud' size='340' side='right'caption='[[3mud]], [[Resolution|resolution]] 2.20&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'>[[3mud]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] 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=3MUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MUD 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3mud|  PDB=3mud  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3mud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mud OCA], [https://pdbe.org/3mud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mud RCSB], [https://www.ebi.ac.uk/pdbsum/3mud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mud ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/XRCC4_HUMAN XRCC4_HUMAN] Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.<ref>PMID:8548796</ref> <ref>PMID:10854421</ref> <ref>PMID:10757784</ref> <ref>PMID:16412978</ref> [https://www.uniprot.org/uniprot/TPM1_CHICK TPM1_CHICK] Binds to actin filaments in muscle and non-muscle cells. Plays a central role, in association with the troponin complex, in the calcium dependent regulation of vertebrate striated muscle contraction. Smooth muscle contraction is regulated by interaction with caldesmon. In non-muscle cells is implicated in stabilizing cytoskeleton actin filaments.
+== 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/mu/3mud_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=3mud ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Tropomyosin is a stereotypical alpha-helical coiled coil that polymerizes to form a filamentous macromolecular assembly that lies on the surface of F-actin. The interaction between the C-terminal and N-terminal segments on adjacent molecules is known as the overlap region. We report here two X-ray structures of the chicken smooth muscle tropomyosin overlap complex. A novel approach was used to stabilize the C-terminal and N-terminal fragments. Globular domains from both the human DNA ligase binding protein XRCC4 and bacteriophage varphi29 scaffolding protein Gp7 were fused to 37 and 28 C-terminal amino acid residues of tropomyosin, respectively, whereas the 29 N-terminal amino acids of tropomyosin were fused to the C-terminal helix bundle of microtubule binding protein EB1. The structures of both the XRCC4 and Gp7 fusion proteins complexed with the N-terminal EB1 fusion contain a very similar helix bundle in the overlap region that encompasses approximately 15 residues. The C-terminal coiled coil opens to allow formation of the helix bundle, which is stabilized by hydrophobic interactions. These structures are similar to that observed in the NMR structure of the rat skeletal overlap complex [Greenfield, N. J., et al. (2006) J. Mol. Biol. 364, 80-96]. The interactions between the N- and C-terminal coiled coils of smooth muscle tropomyosin show significant curvature, which differs somewhat between the two structures and implies flexibility in the overlap complex, at least in solution. This is likely an important attribute that allows tropomyosin to assemble around the actin filaments. These structures provide a molecular explanation for the role of N-acetylation in the assembly of native tropomyosin.
-===Structure of the Tropomyosin Overlap Complex from Chicken Smooth Muscle===
+Structure of the tropomyosin overlap complex from chicken smooth muscle: insight into the diversity of N-terminal recognition .,Frye J, Klenchin VA, Rayment I Biochemistry. 2010 Jun 15;49(23):4908-20. PMID:20465283<ref>PMID:20465283</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3mud" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20465283}}, adds the Publication Abstract to the page
+*[[Tropomyosin|Tropomyosin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20465283 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20465283}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Gallus gallus]]
-MUD is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Gallus_gallus,_homo_sapiens Gallus gallus, homo sapiens] and [http://en.wikipedia.org/wiki/Homo_sapiens,gallus_gallus Homo sapiens,gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MUD OCA].
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
-==Reference==
+[[Category: Frye J]]
-<ref group="xtra">PMID:20465283</ref><references group="xtra"/>
+[[Category: Klenchin VA]]
-[[Category: Gallus gallus, homo sapiens]]
+[[Category: Rayment I]]
-[[Category: Homo sapiens,gallus gallus]]
-[[Category: Frye, J.]]
-[[Category: Klenchin, V A.]]
-[[Category: Rayment, I.]]
-[[Category: Coiled-coil]]
-[[Category: Contractile protein]]
-[[Category: Overlap complex]]
-[[Category: Tropomysoin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 23 08:52:34 2010''