2rpi: Difference between revisions

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-{{Seed}}
-[[Image:2rpi.jpg|left|200px]]
-<!--
+==The NMR structure of the submillisecond folding intermediate of the Thermus thermophilus ribonuclease H==
-The line below this paragraph, containing "STRUCTURE_2rpi", creates the "Structure Box" on the page.
+<StructureSection load='2rpi' size='340' side='right'caption='[[2rpi]]' 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'>[[2rpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RPI 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">Solution NMR</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=2rpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rpi OCA], [https://pdbe.org/2rpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rpi RCSB], [https://www.ebi.ac.uk/pdbsum/2rpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rpi ProSAT]</span></td></tr>
-{{STRUCTURE_2rpi|  PDB=2rpi  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNH_THET8 RNH_THET8] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
+== 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/rp/2rpi_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=2rpi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Elucidation of the high-resolution structures of folding intermediates is a necessary but difficult step toward the ultimate understanding of the mechanism of protein folding. Here, using hydrogen-exchange-directed protein engineering, we populated the folding intermediate of the Thermus thermophilus ribonuclease H, which forms before the rate-limiting transition state, by removing the unfolded regions of the intermediate, including an alpha-helix and two beta-strands (51 folded residues). Using multidimensional NMR, we solved the structure of this intermediate mimic to an atomic resolution (backbone rmsd, 0.51 A). It has a native-like backbone topology and shows some local deviations from the native structure, revealing that the structure of the folded region of an early folding intermediate can be as well defined as the native structure. The topological parameters calculated from the structures of the intermediate mimic and the native state predict that the intermediate should fold on a millisecond time scale or less and form much faster than the native state. Other factors that may lead to the slow folding of the native state and the accumulation of the intermediate before the rate-limiting transition state are also discussed.
-===The NMR structure of the submillisecond folding intermediate of the Thermus thermophilus ribonuclease H===
+The high-resolution NMR structure of the early folding intermediate of the Thermus thermophilus ribonuclease H.,Zhou Z, Feng H, Ghirlando R, Bai Y J Mol Biol. 2008 Dec 12;384(2):531-9. Epub 2008 Sep 26. PMID:18848567<ref>PMID:18848567</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2rpi" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18848567}}, adds the Publication Abstract to the page
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18848567 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18848567}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-RPI is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RPI OCA].
+[[Category: Thermus thermophilus HB8]]
+[[Category: Bai Y]]
-==Reference==
+[[Category: Feng H]]
-<ref group="xtra">PMID:18848567</ref><references group="xtra"/>
+[[Category: Zhou Z]]
-[[Category: Ribonuclease H]]
-[[Category: Thermus thermophilus hb8]]
-[[Category: Bai, Y.]]
-[[Category: Feng, H.]]
-[[Category: Zhou, Z.]]
-[[Category: Endonuclease]]
-[[Category: High-resolution structure]]
-[[Category: Hydrolase]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Nuclease]]
-[[Category: Submillisecond folding intermediate]]
-[[Category: Thermus thermophilus ribonuclease h]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr  2 15:29:44 2009''