1w2b: Difference between revisions

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-[[Image:1w2b.gif|left|200px]]<br /><applet load="1w2b" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1w2b, resolution 3.50&Aring;" />
-'''TRIGGER FACTOR RIBOSOME BINDING DOMAIN IN COMPLEX WITH 50S'''<br />
-==Overview==
+==Trigger Factor ribosome binding domain in complex with 50S==
-During protein biosynthesis, nascent polypeptide chains that emerge from, the ribosomal exit tunnel encounter ribosome-associated chaperones, which, assist their folding to the native state. Here we present a 2.7 A crystal, structure of Escherichia coli trigger factor, the best-characterized, chaperone of this type, together with the structure of its, ribosome-binding domain in complex with the Haloarcula marismortui large, ribosomal subunit. Trigger factor adopts a unique conformation resembling, a crouching dragon with separated domains forming the amino-terminal, ribosome-binding 'tail', the peptidyl-prolyl isomerase 'head', the, carboxy-terminal 'arms' and connecting regions building up the 'back'., From its attachment point on the ribosome, trigger factor projects the, extended domains over the exit of the ribosomal tunnel, creating a, protected folding space where nascent polypeptides may be shielded from, proteases and aggregation. This study sheds new light on our understanding, of co-translational protein folding, and suggests an unexpected mechanism, of action for ribosome-associated chaperones.
+<StructureSection load='1w2b' size='340' side='right'caption='[[1w2b]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1w2b]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W2B FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1w2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w2b OCA], [https://pdbe.org/1w2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w2b RCSB], [https://www.ebi.ac.uk/pdbsum/1w2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w2b ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629]
+== 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/w2/1w2b_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=1w2b ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+During protein biosynthesis, nascent polypeptide chains that emerge from the ribosomal exit tunnel encounter ribosome-associated chaperones, which assist their folding to the native state. Here we present a 2.7 A crystal structure of Escherichia coli trigger factor, the best-characterized chaperone of this type, together with the structure of its ribosome-binding domain in complex with the Haloarcula marismortui large ribosomal subunit. Trigger factor adopts a unique conformation resembling a crouching dragon with separated domains forming the amino-terminal ribosome-binding 'tail', the peptidyl-prolyl isomerase 'head', the carboxy-terminal 'arms' and connecting regions building up the 'back'. From its attachment point on the ribosome, trigger factor projects the extended domains over the exit of the ribosomal tunnel, creating a protected folding space where nascent polypeptides may be shielded from proteases and aggregation. This study sheds new light on our understanding of co-translational protein folding, and suggests an unexpected mechanism of action for ribosome-associated chaperones.
-==About this Structure==
+Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins.,Ferbitz L, Maier T, Patzelt H, Bukau B, Deuerling E, Ban N Nature. 2004 Sep 30;431(7008):590-6. Epub 2004 Aug 29. PMID:15334087<ref>PMID:15334087</ref>
-W2B is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=K:'>K</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=CD:'>CD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=AC1:Cl+Binding+Site+For+Chain+0'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W2B OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins., Ferbitz L, Maier T, Patzelt H, Bukau B, Deuerling E, Ban N, Nature. 2004 Sep 30;431(7008):590-6. Epub 2004 Aug 29. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15334087 15334087]
+</div>
+<div class="pdbe-citations 1w2b" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribosome 3D structures|Ribosome 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
 [[Category: Haloarcula marismortui]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Ban, N.]]
+[[Category: Ban N]]
-[[Category: Bukau, B.]]
+[[Category: Bukau B]]
-[[Category: Deuerling, E.]]
+[[Category: Deuerling E]]
-[[Category: Ferbitz, L.]]
+[[Category: Ferbitz L]]
-[[Category: Maier, T.]]
+[[Category: Maier T]]
-[[Category: Patzelt, H.]]
+[[Category: Patzelt H]]
-[[Category: CD]]
-[[Category: CL]]
-[[Category: K]]
-[[Category: MG]]
-[[Category: NA]]
-[[Category: chaperone]]
-[[Category: cotranslational folding]]
-[[Category: nascent chain]]
-[[Category: ribosomal protein]]
-[[Category: ribosome]]
-[[Category: ribosome_associated factors]]
-[[Category: rna-binding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 10:18:24 2008''