1w2b: Difference between revisions

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-[[Image:1w2b.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1w2b", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1w2b|  PDB=1w2b  |  SCENE=  }}
-'''TRIGGER FACTOR RIBOSOME BINDING DOMAIN IN COMPLEX WITH 50S'''
+==Trigger Factor ribosome binding domain in complex with 50S==
+<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.
-==Overview==
+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>
-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==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-W2B is a [[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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W2B OCA].
+</div>
+<div class="pdbe-citations 1w2b" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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://www.ncbi.nlm.nih.gov/pubmed/15334087 15334087]
+*[[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: Chaperone]]
-[[Category: Cotranslational folding]]
-[[Category: Nascent chain]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome]]
-[[Category: Ribosome_associated factor]]
-[[Category: Rna-binding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 13:03:22 2008''