3ice: Difference between revisions

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-[[Image:3ice.png|left|200px]]
-{{STRUCTURE_3ice|  PDB=3ice  |  SCENE=  }}
+==Rho transcription termination factor bound to RNA and ADP-BeF3==
+<StructureSection load='3ice' size='340' side='right'caption='[[3ice]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ice]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ICE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ICE 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]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</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=3ice FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ice OCA], [https://pdbe.org/3ice PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ice RCSB], [https://www.ebi.ac.uk/pdbsum/3ice PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ice ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RHO_ECOLI RHO_ECOLI] Facilitates transcription termination by a mechanism that involves rho binding to the nascent RNA, activation of rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. RNA-dependent NTPAse which utilizes all four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01884]
+== 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/ic/3ice_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3ice ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hexameric helicases couple ATP hydrolysis to processive separation of nucleic acid duplexes, a process critical for gene expression, DNA replication, and repair. All hexameric helicases fall into two families with opposing translocation polarities: the 3'--&gt;5' AAA+ and 5'--&gt;3' RecA-like enzymes. To understand how a RecA-like hexameric helicase engages and translocates along substrate, we determined the structure of the E. coli Rho transcription termination factor bound to RNA and nucleotide. Interior nucleic acid-binding elements spiral around six bases of RNA in a manner unexpectedly reminiscent of an AAA+ helicase, the papillomavirus E1 protein. Four distinct ATP-binding states, representing potential catalytic intermediates, are coupled to RNA positioning through a complex allosteric network. Comparative studies with E1 suggest that RecA and AAA+ hexameric helicases use different portions of their chemomechanical cycle for translocating nucleic acid and track in opposite directions by reversing the firing order of ATPase sites around the hexameric ring. For a video summary of this article, see the PaperFlick file with the Supplemental Data available online.
-===Rho transcription termination factor bound to RNA and ADP-BeF3===
+Running in reverse: the structural basis for translocation polarity in hexameric helicases.,Thomsen ND, Berger JM Cell. 2009 Oct 30;139(3):523-34. PMID:19879839<ref>PMID:19879839</ref>
-{{ABSTRACT_PUBMED_19879839}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3ice" style="background-color:#fffaf0;"></div>
-[[3ice]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ICE OCA].
 ==See Also==
-*[[Helicase|Helicase]]
+*[[Helicase 3D structures|Helicase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019879839</ref><references group="xtra"/>
+__TOC__
-[[Category: Escherichia coli k-12]]
+</StructureSection>
-[[Category: Berger, J M.]]
+[[Category: Escherichia coli K-12]]
-[[Category: Thomsen, N D.]]
+[[Category: Large Structures]]
-[[Category: Atp-binding]]
+[[Category: Berger JM]]
-[[Category: Atpase]]
+[[Category: Thomsen ND]]
-[[Category: Helicase]]
-[[Category: Hexamer]]
-[[Category: Hydrolase]]
-[[Category: Motor]]
-[[Category: Nucleotide-binding]]
-[[Category: Ob fold]]
-[[Category: Reca]]
-[[Category: Rna]]
-[[Category: Rna-binding]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription regulator-rna complex]]
-[[Category: Transcription termination]]