1m8v: Difference between revisions

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-{{Seed}}
-[[Image:1m8v.png|left|200px]]
-<!--
+==Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer==
-The line below this paragraph, containing "STRUCTURE_1m8v", creates the "Structure Box" on the page.
+<StructureSection load='1m8v' size='340' side='right'caption='[[1m8v]], [[Resolution|resolution]] 2.60&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'>[[1m8v]] is a 21 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M8V 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]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
-{{STRUCTURE_1m8v|  PDB=1m8v  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m8v OCA], [https://pdbe.org/1m8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m8v RCSB], [https://www.ebi.ac.uk/pdbsum/1m8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m8v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RUXX_PYRAB RUXX_PYRAB]
+== 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/m8/1m8v_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=1m8v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. Their proposed function is to mediate RNA-RNA interactions. We present here the crystal structures of Pyrococcus abyssi Sm protein (PA-Sm1) and its complex with a uridine heptamer. The overall structure of the protein complex, a heptameric ring with a central cavity, is similar to that proposed for the eukaryotic Sm core complex and found for other archaeal Sm proteins. RNA molecules bind to the protein at two different sites. They interact specifically inside the ring with three highly conserved residues, defining the uridine-binding pocket. In addition, nucleotides also interact on the surface formed by the N-terminal alpha-helix as well as a conserved aromatic residue in beta-strand 2 of the PA-Sm1 protein. The mutation of this conserved aromatic residue shows the importance of this second site for the discrimination between RNA sequences. Given the high structural homology between archaeal and eukaryotic Sm proteins, the PA-Sm1.RNA complex provides a model for how the small nuclear RNA contacts the Sm proteins in the Sm core. In addition, it suggests how Sm proteins might exert their function as modulators of RNA-RNA interactions.
-===Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer===
+Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya.,Thore S, Mayer C, Sauter C, Weeks S, Suck D J Biol Chem. 2003 Jan 10;278(2):1239-47. Epub 2002 Oct 29. PMID:12409299<ref>PMID:12409299</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1m8v" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12409299}}, adds the Publication Abstract to the page
+*[[Sm-like protein|Sm-like protein]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12409299 is the PubMed ID number.
+*[[Sm-like protein 3D structures|Sm-like protein 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_12409299}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-M8V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M8V OCA].
+[[Category: Large Structures]]
-==Reference==
-Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya., Thore S, Mayer C, Sauter C, Weeks S, Suck D, J Biol Chem. 2003 Jan 10;278(2):1239-47. Epub 2002 Oct 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12409299 12409299]
 [[Category: Pyrococcus abyssi]]
-[[Category: Single protein]]
+[[Category: Mayer C]]
-[[Category: Mayer, C.]]
+[[Category: Sauter C]]
-[[Category: Sauter, C.]]
+[[Category: Suck D]]
-[[Category: Suck, D.]]
+[[Category: Thore S]]
-[[Category: Thore, S.]]
+[[Category: Weeks S]]
-[[Category: Weeks, S.]]
-[[Category: Protein-rna complex]]
-[[Category: Sm protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 23:27:34 2008''