1loj: Difference between revisions

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-{{Seed}}
-[[Image:1loj.png|left|200px]]
-<!--
+==Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP)==
-The line below this paragraph, containing "STRUCTURE_1loj", creates the "Structure Box" on the page.
+<StructureSection load='1loj' size='340' side='right'caption='[[1loj]], [[Resolution|resolution]] 1.90&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'>[[1loj]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LOJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LOJ 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene>, <scene name='pdbligand=URI:URIDINE'>URI</scene></td></tr>
-{{STRUCTURE_1loj|  PDB=1loj  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1loj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1loj OCA], [https://pdbe.org/1loj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1loj RCSB], [https://www.ebi.ac.uk/pdbsum/1loj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1loj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RUXX_METTH RUXX_METTH]
+== 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/lo/1loj_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=1loj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Intron splicing is a prime example of the many types of RNA processing catalyzed by small nuclear ribonucleoprotein (snRNP) complexes. Sm proteins form the cores of most snRNPs, and thus to learn principles of snRNP assembly we characterized the oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs) from Pyrobaculum aerophilum (Pae) and Methanobacterium thermautotrophicum (Mth). Ultracentrifugation shows that Mth SmAP1 is exclusively heptameric in solution, whereas Pae SmAP1 forms either disulfide-bonded 14-mers or sub-heptameric states (depending on the redox potential). By electron microscopy, we show that Pae and Mth SmAP1 polymerize into bundles of well ordered fibers that probably form by head-to-tail stacking of heptamers. The crystallographic results reported here corroborate these findings by showing heptamers and 14-mers of both Mth and Pae SmAP1 in four new crystal forms. The 1.9 A-resolution structure of Mth SmAP1 bound to uridine-5'-monophosphate (UMP) reveals conserved ligand-binding sites. The likely RNA binding site in Mth agrees with that determined for Archaeoglobus fulgidus (Afu) SmAP1. Finally, we found that both Pae and Mth SmAP1 gel-shift negatively supercoiled DNA. These results distinguish SmAPs from eukaryotic Sm proteins and suggest that SmAPs have a generic single-stranded nucleic acid-binding activity.
-===Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP)===
+The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs).,Mura C, Kozhukhovsky A, Gingery M, Phillips M, Eisenberg D Protein Sci. 2003 Apr;12(4):832-47. PMID:12649441<ref>PMID:12649441</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1loj" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12649441}}, adds the Publication Abstract to the page
+*[[Sm-like protein 3D structures|Sm-like protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12649441 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12649441}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-LOJ is a 14 chains structure of sequences from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LOJ OCA].
+[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
+[[Category: Eisenberg D]]
-==Reference==
+[[Category: Kozhukhovsky A]]
-<ref group="xtra">PMID:12649441</ref><references group="xtra"/>
+[[Category: Mura C]]
-[[Category: Methanothermobacter thermautotrophicus]]
-[[Category: Eisenberg, D.]]
-[[Category: Kozhukhovsky, A.]]
-[[Category: Mura, C.]]
-[[Category: Beta barrel]]
-[[Category: Heptameric toroid]]
-[[Category: Ob-fold]]
-[[Category: Tetradecamer]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:25:20 2009''